Hi there, I'm new here, so not quite certain the best way to give feedback. For horror, art style and sound design go a long way. I like your art style in the sense that it's easy to distinguish between units, objects, and the background (It's a pet peeve of mine when there's too much chaos on screen to tell what's going on even when standing still). However everything seems really bright and colorful, so I don't know if there's a way to tone that down a bit. Maybe instead of having all the sprites fully lit, only light the outline around them?
One of the scariest top-down games I've ever played is
Darkwood. It's not a RTS game, but it is a real-time top-down with resource management. One of the things that makes it scary is the vision cone, you can see aspects of the environment that you are not directly looking at, but when you look at things, they will update with "real-time" information such as showing objects, corpses, or enemies. It looks like you have a little fog of war going with lights being on or off. I would try adding different levels of vision cones to see how that affects gameplay. I know the point of RTS games is to have near perfect information in order to make decisions, however I think that removing that information can make things more uncertain, and thus scarier. You could try having only rooms visible that units are standing in or that they can see into (for instance one of your screenshots shows a visible room on the other side of a closed door. If the door is closed, the room should be a mystery), or you could give individual units their own vision cones based on the direction they're facing (play around with large fov or narrow fov), everything in the vision cone is "real-time", and everything outside the vision cone is a little darker, and does not display enemies, only the basic info about the room itself (floor, walls, doors). Combine the vision cone with the lighting system you already seem to have: If a unit is looking down a hallway, the hallway still needs to be lit to see anything in it.
Another scary aspect of Darkwood is surviving the darkest part of night. I have no idea what's outside at night, I don't want to know, my only choice is to lock myself in, stay close to the light, and hope. Perhaps some kind of "insta-kill" fog that slowly closes in and surrounds the map as long as there are enemies remaining, and only light keeps it at bay? Or just make wandering into darkness itself is deadly, with patches of Fog so thick that flashlights don't penetrate it, and you have to disperse it somehow? A daylight meter in itself can give you a mission clock, because at night when the fog comes, a lot of enemies spawn inside the fog, so you have to be boarded up and locked-down with enough supplies before then. It looks like you have an overworld map, so perhaps the arc of the game is to simply get across town, and you can only move between buildings during the day (still not 100% safe), and then camp each building at nightfall hoping to survive. I dunno, just ideas.
Another scary game (which I haven't played but watched) is
Duskers. It's a real-time strategy game about managing salvage drones aboard derelict spacecraft. It is scary mostly because you lack a lot of information, everything's abstract and you navigate mostly with schematics only. You only get to know what's in a room for sure if you move a unit into it, however there are motion sensors and computer consoles you can interact with that show you which rooms have movement in them. So you want to make sure a room is as safe as possible to enter before opening a door, so you plan you moves carefully. This leads to very tense moments of trying to open doors remotely, trying to get "whatever is in there" to move to a different room, and then locking them in. And don't you dare open an active room directly adjacent to your units. There are also vents that the enemies can move though to connect different rooms in unexpected ways, and you have to read the schematics carefully (or infer their existence if schematics are incomplete) to catch them. So Duskers has a high level of abstraction from the enemies (you rarely get to see them until it's too late) and it has a "plan carefully/things are not going to plan" loop that looks very scary.
I would try to abstract enemies as much as possible in your game until you absolutely can't. So maybe try removing the taunting enemy dialogue boxes when they are in shadow, which lets you know something is there for sure; It's always scarier not knowing. Maybe you can have enemies make footstep sounds, but all your units need to be inactive for things to be quiet enough to hear. Maybe they are not directional sounds, you just know somewhere on the map something is moving around, but not where. It looks like the structures you are in have traditional doors, but maybe there could be a research facility later that has automated doors that you can control remotely from a console in the style of Duskers, trying to figure out where enemies are and manage around them, with not enough resources (ammo/health) to survive too many direct enemy encounters (you can't brute force your way through all the enemies, only a handful).
edit: Found the video I watched that made me want to try Duskers, just haven't had a chance yet. It makes a strong argument and am certain I would get spooked.
I love how one of you inspirations is Aliens. Part of the genius of the xenomorph design is that they are dark color, with strange indistinguishable mechanical shapes all over their bodies, so when you get a flash of one in the dark, you can't really tell what you've seen. I see some good enemy variety here, but for a really spooky creature, try a shadow monster or two, with fuzzy ill-defined edges, and AI that reacts very infrequently until they are well-lit, and will move around and relocate in darkness. They will blend into the shadow areas, so if you catch a glimpse of one, you can never be quite sure what you've seen, and if you go back for a second look, maybe it won't be there.
Another idea is some mimic type enemies. Regular office chairs are scary as hell if they're really a monster in disguise.
Also, perhaps a sanity meters? If a unit is almost totally insane, it won't respond to your commands and could hurt friendly units. As the meter rises, you get a higher percentage chance of a disobeyed, or delayed response to commands. You could have some kind of nerve calming resource as well, which gives you more reason to explore unsafe areas, and more hard choices to make when you have limited supply. Slowly dropping sanity can be a mission clock on its own and put pressure on players to make quick and poor decisions. I feel that the Eldritch style Madness meter can be overplayed, but it is an effective trope. While you want your game to be "fun" to play, some elements of effective horror rely on wearing down the audience in a way that makes them continuously anxious. You need breaks from the anxiousness from time to time (pacing is important, but in games the break comes naturally between missions), but you also need to apply the pressure to affect an oppressive atmosphere. Finding the line is a balance issue for sure.
If not a sanity meter, you could just replace it with hunger/food. If your balance and delivery are good enough, the real sanity meter is the one inside the player's head, slowly unraveling as they loose control over the situation. I'd be careful about adding too many types of resources, otherwise it will become a resource management game (unless that's what you want), but something to keep the pressure on other than just heath and ammo. RTS games are all about being able to multi-task and split focus anyway, the more the focus is split, the more anxiety there is as situations happen faster than they can be responded to. Too much split focus and it can become frustrating, but too little and the player won't be nervous enough. (A couple of examples of games that can drive a player mad with worry are Tharsis and Darkest Dungeon, which aren't necessarily considered horror games, but induce high levels of anxiety to be horrific in their own right).
Another thought is that balancing pressure on the player is critical to horror games. It has to be just right. One game that really comes to mind is [spoiler]Resident Evil 4[/spoiler]. It's a bit of a spoiler, but the game has a hidden auto-balancing mechanic. Many games have done this, but this is the example that comes to mind first for me since I've replayed it so much. Basically, resources (ammo, health, money) are mostly loot-based, from both enemies and breakable boxes. If you are doing well and killing enemies easily, the game gives you less resources. If you are dying a lot, the game will drop loot more frequently. This system works because it's invisible, it's not telegraphed to the player, all the player knows is that "I only have 12 bullets left". And if the auto-balance is working right, the player should constantly have *just* enough resources to get by, but never more.
Hope some of that helped