I’ve never used pallets myself. I’m too chicken. From the possibility of tearing up your blades, to all the hoopla about chemicals and such in the wood (I hate wearing respirators, or even simple masks, though my wife makes me sometimes!). Also, most of the pallets I come across are just pine, and usually they are rotted. That being said, I don’t think its such a bad thing to have those nail holes. They don’t look bad. Show them off. Be proud of them. You’ve got that “reclaimed lumber” tag going for you, and the wood really is looking good!