even not regularly is overestimated hehe jk
when you are sure you are done with modding you can delete (or better back up to pc) everything except your apps folder and usbloader folder (and whatever you have in images), recheck what in the config folder is (think something for MMM or similar program, if app is unused delete too)
apps can be cleaned from apps you don't run/use anymore.
all that won't interfer with your hbc loading or something.
new apps go in the apps folder of course.
good luck, have fun playing / further modding