I'm on version 6.21 of mIRC. Let's say I wanted to update to the latest version. Will all of my scripts and settings(auto join, perform, all the configurations) stay in tact, or will I have to reload/reset everything?

As long as you use the Update option in the installer, everything should work as it currently does. If something stops working, check the bug reports section to see if the problem has already been reported.