Each ship can be 5-100kb big, and eventually it adds up after a while, but 95MB does seem a bit excessive.
If you've got the "sqlite3 shell" program installed from http://www.sqlite.org/download.html, you could try running this, although this is something the server should be doing in the first place:
sqlite3 KMP_universe.db VACUUM
I'll find out if there is any other entries that can be deleted, having a database that big wasn't too uncommon in the past.