I had around 34 hacks installed, plus a few custom tweaks..
I've ran the upgrade script and re-modified the changed templates and haven't run in to any problems so far.. I'm currently in the middle of re-adding the file changes for the hacks.
I'm in the process of upgrading from rc4 to 3.0.3. The upgrade scripts went flawlessly as expected (I have a ton of hacks installed too). Next comes reinstalling all those hacks and doing the template edits and praying that everything will still work right.