[EagleOCNJ]

I agree you should grind them out. Ive had some big blisters on another boat where I drilled them out and they drained smelly water. Ive encountered others that seem to be like what you describe and they may just be a result of air void. Grind them out and verify that they are dry. Next when you know its dry, thicken up some west system with collidal silica and trowel it on with a spackle knife.

If these are deep and large youll need to add some fiberglass cloth first though. You really need to post some pics and describe them better, indicate dampness, etc.

After the hull is stripped and repaired correctly then definitely do the interprotect system. I always do that in your situation; why not you have a clean bottom to start with! I usually use less than the manufacturer recommends, say three coats and you can usually do all three in one day with decent weather.