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3,695 zip files is very high! I rarely go over 100 zip files unless one of my machines is off the net for a few days or I do some massive reorganization. Take a look at the Show Clients display in OmniFocus' Sync preferences pane. Are there any entries that show clients that haven't been synced in the last day or two?

Assuming you don't have any spurious client entries (which should generate the occasional warning message from OmniFocus on the desktop after they haven't synced for a week), the database should compact automatically in normal use. It might not, however, if you tend not to leave OmniFocus running when you aren't actively using it. If you start up OmniFocus on the desktop, click the Sync button, then do the same on your iPhone, wait 61 minutes and do it again (syncing both machines) you should see a compaction. The sync process won't consider compacting anything less than an hour old, and will only compact changes that have been incorporated by all of the clients. This compaction seems to happen more readily when the desktop client can do its hourly syncs.