I don't want to disable them. I've gotten attached to them. It's pretty much the way I read email. I go down my search folders one-by one (well, the ones that have new mail). Then finally I read the "Unmatched" folder.
With Evolution 2.24, the message count on the search folders was wrong 99% of the time. Some folders will show as having new mail when there is none there while others show no new mail when there is. And the Unmatched search folder was removed. Then you would get wacky things like "111/-3498 unread messages". Basically the search folders became useless, which is why I'm still using Evo 2.22 even though the rest of my GNOME desktop is 2.24.