I'm not sure if I can follow you here. The reason they have their own skill is so people don't use them as secondaries which would probably be the case if they were paired with other ranged weapons. From logical perspective it also makes sense to have them their own skill. Just because crossbows can be aimed as firearms it doesn't involve the same handling. A crossbow is simply a horizontally aligned bow with a trigger mechanism that holds the draw for the shooter. Projectiles fired from bow or xbow both have the same speed, energy and trajectory which declines faster than with firearms and therefore can't be shot as flatly.
The change I would make is have them penetrate thick vests by ignoring damage threshold. Despite being slow projectiles they are very sharp and don't deform like bullets on impact. Sledgehammers do the same now but for different logical reasons, they don't penetrate a vest but their weight transfers all the energy through. To compesate for this advantage I'd make crossbows generally a bit weaker.
They're still good right now. When it comes to balance compared to other weapons, think about it this way. What are usually the most annoying/dangerous enemies in the game? To me it's the crossbow and sledgehammer guys. Both hit hard, penetrate shields and can cause stun. If the AI can make a good use of them, you as a player are even more capable to do so.
There is no single weapon class in Underrail that I can say is absolutely inferior. Sure, balance wise the weapons are not 100% equal but this is not a MMO type of a game. The strength differences are never big.
This is also true for crossbows but they require a more effort and strategic approach then other weapons - crafting special arrows, traps and sneaking is a must. Quick tinkering and deadly snares is so good it's crazy.
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