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If you're referring to the zip file count as the source for your concern, you can relax a bit. There's a zip file created every time you make a change to your database (sometimes you'll get multiple items changed in a single zip file). These zip files are periodically compacted by the sync process once all of the clients have digested them as past history. You can get what seems like an outlandish number of zip files if you make a lot of changes in a short time but they won't stay around if you sync regularly. If you simply launch OmniFocus on both Mac and iPhone and sync both of them once a day, you should never have more than a day's zip files hanging around.

OmniFocus will automatically suggest archiving your completed actions and projects to the Archive database, I think on a monthly basis. If you agree, they are removed from your active database. You can also make this happen on demand with the File->Move Old Data to Archive... command. You can also just pull up the Completed perspective and delete anything there you no longer want prior to (or instead of) running the archive command (for example, you might not records of grocery shopping tasks, but details of some project you did for work might come in handy at review time).