I don't know that I (or anyone) can really answer your question, but here's my current thoughts on the topic.
My 'regular' course has water on every hole, most of it lateral in the areas that most courses would have rough, or maybe OB. So lost balls are a regular occurance, even for better players which I'm not. The pro shop sells a LOT more used balls than new, and the best and most expensive of the used balls are Pro V1s. I've noticed that the used Pro V1s are about the same price as new NXT Tour balls (in my local shop, your milage may vary.)
The used balls look good, but I've been told by reputable sources that most of them come out of the water "somewhere." How long they were in the water is, of course, a mystery. However, I expect that enough osmosis (water seepage) would occure to significantly affect the ball's performance before the cover actually discolored much if any. If cost is an issue (when isn't it?) you might consider playing the NXT's just to guard against the 'dead' ball that's been in the water too long, even if it looks good. Otherwise, if you're concerned about the used balls, bite the bullet and play the good stuff.
Anyone with real information on exactly how waterproof modern balls are?