Any ideas whether it will be fixed for the next update?
As many of these problems survived several updates, my guess would be no. Some hints on the cause can be found here:
http://hydlaa.com/smf/index.php?topic=23617.msg259907#msg259907which at least had the problem with the ladder in the tower and the laanx well dissappear. For the other known places, just be carefull not to walk into the gap

. For example, the sewer exit gap is to the side of the stairs, and can easily be avoided by walking up the stairs all the way to the rock, and then follow the rock to the side.
I am not sure, but I vaguely remember that these problems are related to the 3D engine, meaning that devs wait for the engine to become better instead of wasting time patching up all locations one by one.
I see someone posted in the meantime:
It is entered in the bug tracker and will be addressed when someone can mod the map. More irking is the falling through the ground in combat issue, I think. But just avoid those areas for now...
Being entered in the bugtracker does not necessarilly mean it will be solved anytime soon (not tm), judging from the above linked thread, the submission date of that bug (march 2005), or the version in which it was first found (0.3.008). It already survived 8 updates.