I'll put my 2 cents in, but I'm sure there are others with lots more info, like JeanneB and Craftymouse to name a couple. Anyway, someone passed on the smartertravel link and I booked a "sale" room at Comfort Suites on Nassau for 176.00 a few days ago. Today, someone passed on a travlezoo link and I was able to book a room at the Atlantis for 179.00 instead. As I understand it, both hotels are owned by Atlantis, and guests at the "less expensive" Comfort Suites have access to the great amenities at the Atlantis. The drill is to check in at CS (and check out at the same time, if you wish) and get your wristbands and head on over to enjoy Atlantis. Difference between 2 hotels is that CS allows 4 to a room and Atlantis allows 5, meaning that this is the number of wristbands you are allowed. So, for me the Atlantis deal was so much better because now, not only do I not have to buy a "day pass" at Atlantis for our 5th family member, I can also just go straight to Atlantis from the boat. I also read other threads that mentioned the availability question of day passes, which I guess could change day to day. I don't know the cost or what you are allowed to use with this type of pass.
Now as for the reason to check into a hotel on a cruise- personal preference. Didn't feel that some Nassau activities were suitable to my kids ages/tastes. Did not want to really venture out on our own. Didn't feel we'd really vacation at Atlantis for extended period of time, although did not know the deals you could get. My kids love water parks, pools, slides. While its an added expense to the cruise, I felt they'd get what they want and I'd feel like I was actually in a part of Nassua, and DH would be happy cuz we're happy! Sorry this post is so long- just trying to explain options/reasons.