Nick, if your boat has delamination or rot in the deck, the only economical way to repair it is for someone who has more time than money to DIY. Any fiberglass shop (auto or marine) that knows how to do this work will be charging a fast $100/hr or more, and there's lots of work.
Do you really need that work...who knows. Check out West System Epoxies online, they have some articles posted about decks and deck repairs that will give you a start to figuring out what you really have.
Since a factory deck doesn't have "paint" (it has gelcoat) the odds are you don't have paint cracks. If only the gelcoat has crazed, which is possible, then you only need to deal with that. If the glass under it has cracked, you have bigger issues. If there has been water penetration and the coring degraded, again, bigger issues.
In terms of saving labor...the only "right" way to redo a deck is indeed to remove all the hardware (lots of time) and reinstall it afterwards. Some folks will leave it on and just mask around it--which still takes lots of time and never is going to look as good afterwards.
Sometimes you can do the core repair from below, but that's not so easy either.
Bottom line? You need to find out what you really have, and then weigh the options. Yes, boats have been thrown out because of deck problems that would cost more to repair than the boat is worth. I spoke to someone about a boat this summer that was beautiful below. Market price on sisterships, $35-40k. Selling price on this one? Less than $18k, because of the amount of deck work needed. The yard that had the boat estimated $20,000 to do the repair "right" in their shop.
Bargain for the buyer? Maybe. Maybe not.