there is a difference between countersinking and de-burring, you definitely want to de-burr those holes.....
as for countersinking if you ask ten different people you will get ten different opinions, i chose to countersink mine because countersunk holes are less likely to crack and because imo it just looks better.
a good way to de-burr your disk would be to go over it with 80 grit sand paper on a DA sander, just make sure you keep the sander moving so you dont create an uneven spot, this will also de-glaze your disk if it needs it.