55 mb is really not that big. I’ve seen db4o files in the multi-gigabytes that perform just fine. And the way that DBs work the size of the DB rarely impacts performance until they get so big they no longer fit into RAM, and even then not much.
I do not know if there is a way to clean the DB, though it seems like some sort of mechanism would be useful for the embedded databases like db4o. Because db4o is an embedded DB it does not appear to have a lot of tools you can use outside of writing your own programs.
One thing you can consider doing is for those Items you have that you don’t care about their historic data at all switch to MapDB. MapDB only saves the most recent value and is particularly useful persisting those Items you only care about for restorOnStartup. That will slow down the growth of your DB significantly.