The holes won't hurt. You need a vapor barrier behind the cbu, or a waterproofer on top of it. If you use one on top of it, then you need to tape and thinset the joints first (assuming you use something like RedGard which is a paint on one). The joints, regardless, should be taped with the cbu specific, alkali resistant mesh tape. It is easier to do this while tiling, otherwise it is easy to make 'speed bumps'. The tape and thinset on the seams is for reinforcement, not looks, so you don't want to create a hump and taper.