Should I upgrade from atv fw 3.0 + atv flash 4.0?

I have an atv with firmware 3.0 running atv flash 4.0. Should I upgrade to the latest atv firmware and atv flash version? Which add-ons am I missing?

You’re not missing much in the AppleTV software, but you can see the aTV Flash version changes here:
http://www.atvflash.com/changelog.php

Is it possible to upgrade to the latest version of atv flash without having to do a clean reinstall? Will the latest version of atv flash work with firmware 3.0?

Yes, you can install aTV Flash updates through the Maintenance --> Manage Plugins menu. If you wish to update the AppleTV system software aTV Flash will need to be reinstalled using a USB flash drive.