So, enemies popping up uninvited through the airducts has been implemented, albeit not as nicely as it could have been. This gives me a couple ideas on refining the idea, though.
1. A somewhat more limited number of airduct openings. Just allowing the aliens to spawn anywhere they please doesn't seem right; sure there may be places for something crawling in the ducts to get out, (in fact, there could be a lot of places to get out) but is there ever an opening to the airducts in every single room of any building? What I'm picturing boils basically down to this: Small rooms, like 4x4's or 5x5's (maybe 6x6's), only have one opening enemies can come out through, and the bigger rooms (like 20x7) will have maybe three or four airduct entrances for aliens, but there will never be a time when you take a single step and suddenly you're surrounded. Instead, the worst you could have (which would still be undeniably game-ending) would be a neverending stream of aliens from the various ducts. You should, of course, also be able to see these ducts, though whether you need to see an alien pop out of one first, need a bit of XP put into Perception first, or can notice the differences straight away is a bit of a toss-up.
2. The ability to seal airduct openings. This is a bit more ambitious and maybe a little unbalancing, but I think that the restrictions make up for this without making the benefits useless. First, it will take a while (maybe.. I dunno, 50 turns without some Technical skill for a normal wall duct, and 75 for the rarer but harder to reach and work with ceiling duct?) to seal up the exit so the aliens can't use the opening anymore, and that means you increase the danger level substantially. Second, if it's a big room you'll have to seal ALL of the exits to keep aliens from coming in, and if you're looking at 5 or 6 entrances that means 250-300 turns just to keep yourself safe in that one room (during which time you could be interrupted halfway through by a stream of enemies coming in through the last couple of entrances). A possible third is that in order to seal entrances in the first place, you'll have to hit the Engineering tower for some sealant. The benefit (being able to seal up a room with nice goodies and/or an elevator room for later, simpler travel) would have to be weighed against the consequences (time used up on sealing a room that might be better used looking for ammo/getting to the Queen).