Yeah, a lived-in look sounds like the best approach. I heard several kids say that they were creeped out being on the Batfish last weekend. It doesn't make them want to come back, again, which is bad for business.
Sound effects piped through the boat would add to the realism of a working boat, as well. Even if you have some pump or electric motor humming noises piped over the speakers and maybe some metal creaking noises, it would make a big difference but you don't want to creep people out. ( ihave a bunch of submarien sound effects on my computer and a memory stick if anyoen wants me to email them to them). "People noises" being played over the speakers (i.e. conversations, tools hitting something metal, etc.) without anybody actually being seen making them would be a creep factor, too. The only exceptions would be a phonograph or radio.
Lighting is another issue. It's probably historical to have 40-watt bulbs in all of the lamps, but if it reminds people of a dungeon with cob webs, then, they aren't in any hurry to come back and show their friends. I like idea of having lights in the lower deck, too. Flourscent bulbs are great for saving energy, as long as they aren't directly visible. I have started looking for clear 60-watt bulbs when I go to the stores.