I've only been on one cruise before (Carnival Splendor) a few months ago (but am going again in a week, I loved it so much!).
I didn't really find any "secret" spots to do it on the ship, but all I can say is that on the upper decks after midnight, there were plenty of opportunities. We actually had a competition to see which couple could have sex in the most spots one night with some friends we made (real mature, I know, but it was late and someone gave me their cheers beverage program card for a night...). We did not win, but we got these:
Glass lobby elevators (quick one of course)
Serenity deck in one of the large chairs on the front
Golf course (grass was soft!!) and on the pirate ship on the course (probably shouldn't have...sorry guys)
On the roof above the golf course where the radar is (realized the next day it was an off access area)
Oral in the dance club in a dark corner in one of the window wells
Lobby area between the elevators on the spa floor
Tried to do it on the outside balcony of the upper lido deck (but chickened out!)
Probably tried elsewhere but the night was hazy...
Also, I want to note that my gf and I are not very sexually adventurous. I'd say we are about average level out of all the couples we met/saw on the ship. Which means, if we did it in these places, people on these cruises must literally be effing everywhere... Probably ran into at least a half dozen people going at while walking around the decks at night over the course of an 8 day cruise.