Since we received no further feedback and benjamin and I have been running our DokuWikis for some time now, I have updated the script at
http://www.dokuwiki.org/tips:maintenance to reflect the recent discussion, i.e. we do not only remove empty directories in "$conf['savedir']/pages/" but also in all the other directories.
However, I have chosen an approach which is a bit safer than the one suggested above. So, the new "find" now is
find "$1"/{attic,cache,index,locks,media,meta,pages,tmp}/ \
-mindepth 1 -type d -empty -print0 | xargs -0r rmdir
In order to make this work I had to change "#!/bin/sh" to "#!/bin/bash". (I assume that if someone really needs a Non-Bash shell they probably know how to rewrite the "find" line.)