Yes there a bad idea. They do a lot of things to the registry that equals deleting. even if that section of the registry is messed up its working in a messed up state, if they delete it, it wont be working at all and if windows does not restore it, with out a backup there is no way to fix the problem with out formating the system.
Also you must remember that these cleaners are third party programs that are not endorsed by microsoft, in fact the warn against them in there support forums.
the reason why is because these registry cleaners don't really know how the registry works 100% so there going to get false positives and delete something you don't want it to.
Im a professional when it comes to editing, deleting, cleaning registries and if i use one of those programs and say yes or no to specific things I could still mess up my system on accident.
A good example of this is Lavasofts Adware, they have a active registry watcher program. If your windows shuts down incorrectly and you boot your system backup it will say windows wants to do something to your registry, if you click no for some odd reason, you will have to reinstall windows most likely. What happened to me was all exe files were not able to be ran and some other bad things.
So from now on I stay away from those programs and just do it manually for things I need to do.. Like remove services that are crashing that have no use anyway. Fixing video card problems. Cleaning out printer drivers that do not fully uninstall. and various other things.