What liveaboard are you on? On many the dive deck is completely covered and there's no need to go into the sun between the dining area and cabins, or if you do it's for a very short time. So you might not even be in the sun unless you make a point of it, perhaps going out on a sundeck between dives. Personally I don't put on sunscreen (except maybe on my face) before a dive, as I'd doubt even most "waterproof" sunscreens will still be doing much after a dive and the wetsuit rubbing on it. Even most waterproof sunscreens say to reapply after being in the water.
As far as affecting a wetsuit, I've heard people say it can be an issue and some say not. Also that a chemical sunscreen is more likely to be a problem than a zinc oxide type sunscreen. I would also say sunscreen that's been on awhile and absorbed (which is the way you're supposed to do it) is less likely to be a problem then just applied.
Note that some people also have strong feelings about using sunscreens that are safer for the reef.
