From what I see about climbing nuts and cams, both look perfectly legal. Drilling is illegal, whether it is to place smooth steel pins, other steel bars, rebar, or climbing bolts. The above/below waterline distinction makes no difference except in the mind of someone trying to justify their criminal actions. After all, it sounds so much better to tell your houseboat guests this fake above/below waterline story rather than to just come out and say, "I care more about my personal convenience than the well-being of the lake and others who use it. As a houseboat captain, I drill holes to make up for my lack of actual boating and anchoring skills."
I had a conversation with an NPS ranger not long ago. I asked how it would ever be possible to prosecute sandstone drillers since the character of someone who would drill stone would so often be the same character and integrity of someone who would tell lies claiming that the holes were already there. NPS now has rules to deal with this. Using drilled holes that were already there is just as illegal (and carries the same criminal penalties) as drilling the holes.