You do NOT have to uninstall and reinstall hacks.
I've successfully upgraded my heavily hacked forums using a file compare program and a good CVS text file that I keep updated.
A bit more work when you install hacks means much much less work when it comes to upgrading.
As for upgrades interfering with hacks - this is always a risk - when you get a db error, you will need to edit the appropriate installxx.php file to change or remove the query and rerun that step again.
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