only thing i don't like about Categories is that i was forgetting to remove apps out of the category folders before i deleted Categories. just made more work for me if i had to restore & re-JB. made my recovery of JB apps a mess, but was fixable.
as an alternative to Categories, i use SpotBright from Cydia/Rock. if you have JB apps, the native Search won't locate them. SpotBright will search app store apps as well as JB apps. this way i can hide app icons on SB, yet find those same apps using search/SpotBright. just another alternative to using Categories. Upside: clean SB look, small amount of pages. Downside: forget an app name, you're S.O.L.