Well put it this way.. if every things there and the ps3 is running, its probably best keeping it that way.

never know what deleting one folder will do. Just keep the little bit extra data and avoid corrupting anything. Wel thats my thought.
adding and deleting games thats fine.
And if u wanna see how much space in it.. just right click and hit properties. (pretty sure u can do that in winscp)