It can hurt to upgrade if Khaled has changed it significantly enough. Sometimes scripts just stop functioning correctly because of changes. Plus, changing the layout seems unnecessary, and I wouldn't want to learn how to navigate it differently.
The most common cause of scripts no longer working is due to poor coding. 6.20 made certain bad coding no longer work, such as missing a closing ) on an IF statement. I personally don't see a reason why that's a problem. If you want to use scripts, then you should either use ones that are updated and fixed regularly, or ones that you can fix yourself. That's just my opinion, of course. New versions of mIRC have caused Invision to stop working and we have fixed those issues quickly. Other major scripts should do the same... either from the original author(s) or from supporters.
As for layout changes, there aren't that many. Yes, options were moved and a few other things at one point. So what? It takes all of about 5 minutes to find and remember where everything is. Besides, I don't know many people who bother going into options from the menu instead of using Alt-O. I think the new features and bug fixes are well worth a few minor layout changes and a few scripts no longer working.