Well, the problem still persists and after some very time consuming tests I seem to have found the cause: it seems to be related to the "stale imap connections" problem in this thread:
viewtopic.php?t=4234
This is how I have come to this conclusion:
If I create a new user, fill his mailbox and immediately delete him again, without ever logging in as said user, the used space gets cleared from the disc immediately after I delete him.
However, if I fill the user's mailbox and then log in and out of it via SWA, that leaves open 2-3 in.imap41d processes on the server that belong to that user. Since I cannot delete him while these exist, they won't disappear by themselves and there doesn't seem to be any proper way to end them, I have to kill them. I can now delete the user but none of the data will be deleted and thus no space freed. This is completely reproducable.
This does not happen if I connect to the mailbox with an IMAP-client, for example Thunderbird. In that case, all imap processes are properly ended after I log out and deletion of the user also clears the data from the disc. Outlook+connector is also no problem. That is, if the user has never logged in via SWA before. The only thing that causes this is SWA.
If I restart Scalix with /etc/init.d/scalix stop/start or omshut/omrc, the imap processes are properly ended and after I log into the SCA and delete the user, the data is deleted properly. However this is not a viable option, I cannot restart the whole server every time I want to delete a user!
In my opinion this seems to be a bug. We would need a proper way to end the imap processes left behind by an SWA session
without restarting the whole server. Unfortunately I don't think I can justify purchasing a commercial version of Scalix in this state.