1) The worst thing that can happen is your phone becomes unstable or you have screen tearing. Restoring a nandroid backup, or even just flashing a different kernel will fix it. There is no harm in it. If you're trying a kernel like netarchy, try more-HAVS first, then try less-HAVS if you have a problem with the first.
2) HAVS is automatic, in that it will automatically change the voltage as it's supposed to as the frequency goes up and down. How the frequency is set under certain conditions is determined by the governor. Each kernel has a default governor. If you don't want to use the default, and pick another governor made available by the kernel, you must use an app that has the ability to change it. Setcpu is one such app. OS Monitor can do it too. There are several others. They just need the ability to run as root, and keep the setting at boot.
3) If you're referring to nandroid backups, then no, you don't need to wipe anything. The fact that the backup is overwriting what's there is generally good enough. If you're the paranoid type (not a bad thing

), go ahead and wipe. It only take a few seconds extra, anyway. As for apps, no matter what you do, if you restore a nandroid backup, whatever apps, settings, etc. you've changed since the backup will be wiped out with whatever was actually backed up.
EDIT: Frenchy beat me to it

. But be aware that HAVS, itself, has nothing to do with load or anything else. It is controlled directly by the CPU frequency. Everything else is up to the governor. As for setcpu profiles, it's the smartass governor that can't be used with them. I think the whole HAVS/setcpu profiles conflict thing is a myth. If it was a problem, you wouldn't be able to use HAVS with the smartass governor, since it does the same thing. My 2 cents.