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There's basically 4 places OmniFocus puts data:
1) The application itself, usually in your Applications folder (this is really a wrapper with a lot of files in it, that's probably what you're seeing copied over).
2) A preferences file for each user, usually in your Library/Preferences folder.
3) The OmniFocus folder in Library/Application Support contains your actual data, and the web interface if you're running it.
4) There's also a cache of your OmniFocus data to speed some things up, stored in Library/Caches

You're over-writing (1) every time you update, and each of these updates will just re-use (2)-(4) from the previous version.

The only real clutter you're going to build up by installing a new version 5 times a day is the disk images you're downloading. Once you've copied the application to your Applications folder (or wherever you like it to live), you can unmount and delete these.