The Tavern

One vault at crypt:3 features a room full of loot, with "cages" made of bars of the left and right side, with each cage containing a lich and a alich. I used a wand of disintegration to open each cage and lure out the liches before entering the vault. When I entered, both cages disappeared. Apparently, it was intended to be a trap. However, this is easily avoided.

Being cheesable if you're intuitive or have had the vault before may or may not be part of the intended design, but that is certainly the case and it's a weird, spoilery vault that should be changed or removed imo.

david_glass_crypt, probably. (The glass was turned into grates years ago.)

I'll confirm that I also always use disint to open them up and kill them before going in. I didn't actually know it was a trap that opened up, I thought they were just supposed to summon demons from behind the grates.

Wouldn't making those walls transparent stone solve the problem?

Yes, that's my vault. The issue can be fixed (for example like Sar suggests) but I am not sure it's necessary.

Even transparent stone can be destroyed by lrd and shatter.

It is necessary IMHO. I was surprised by the vault just once, after that I always disintegrate the grates and fight one lich at a time. 2 liches are not just twice more dangerous than 1 lich, they are much more dangerous

Isn't there tons of vaults like this, that can be "cheesed" in some way? Always thought it was intended behavior, rewarding player ingenuity.

(Example: the bailey one with the returning tomahawks that can be trivialized if you have access to flight.)

It's pretty obvious that you can mess up those kobolds by flying or shooting or just stalling them out of ammo even if it's your first time doing that bailey.

In the case of this crypt vault, if you haven't seen it before, you have no way of knowing that some walls about to just poof away and put you in a very bad position, but if you do know that then you can break some walls in advance to avoid the danger.

Autoexplore trap.

It is not autoexplore trap, as the liches prevent you from doing that.