the monsters are all dead (they disappeared), he doesn't have to "climb" it again.

well ok, they have to climb, but without monsters or any resistance.
Unless they have a respawn timer :/

But there is something which is still very confusing... I thought the tower would collapse after the defeat of druaga and so Kaaya + Neeba are basically cut of from the rest... but the tower seems to be still intact.

And why were they flushed out anyways? I mean it's somehow odd that only the upper celling (where all the loot is) is flushed and even collapsed... this was really only done to separate Jil from Kaaya+Neeba.

Plus, I wonder if the rest did actually survive that water-ride (Coopa etc)