Every time a missile has hit a hangar, my craft has been destroyed in previous versions, craft armaments included. I don't think the ruined hangar change would change this since it's hangar capacity is 0. I actually always sell the codex hull in jack sparrow because of the missiles because of this, it's pretty annoying.
That said, facilities seem to be able to survive a lot of damage in base defense, to the point that I'm not even sure the vanilla mechanic even works in x-piratez or was removed or something. I remember my base being blasted to hell with blaster launchers and plasma and not seeing anything destroyed. People use barrel bombs all the time, and the main concern is usually whether or not it blows up inventory.
Edit:
Assuming oxce inherited vanilla mechanics, I found this on ufopaedia:
"
Doing too much damage to a room can also collapse it, and you will lose that room permanently. Any rooms that can only be accessed by going through the collapsed room will also be lost. Spawn-point rooms such as Living Quarters, Stores, Access Lift, and Hangars (plus the Alien Containment chamber) can't be collapsed."
Given gals seem to spawn darn near everywhere, I'm curious what facilities actually aren't safe if this is true.
Actually, maybe this is why I've never seen it happen, from ufopaedia:
"Fortunately, these tiles only exist on the upper floors of your base, and the aliens make no attempt to target them once they encounter your troops (... if they don't encounter your troops, they'll spend the first few dozen turns beelining these tiles - and if they're allowed to reach one under the CE version of the game, when they fire it'll crash). While explosions on the lower floors may damage the upper flooring, they leave the furnishings unscathed - even if the floor gives way completely, they'll still hang safely in midair. Presumably the builders had the foresight to attach them to the ceiling with wires."
