Like Alex (and others), I always pack my dome port in checked luggage. (Good idea about the cake/hat box for packing the Superdome; I'll have to try that!) Unlike many people, however, I don't pack just cameras/lenses in carry-ons, and most of my UW stuff in the checked bags.
Being a firm believer in the "sh*t happens" principle, my philosophy is that I want to be sure I have in my carry-ons enough gear to do "some" type of photography for a whole trip if my checked bags never show up (or are broken into and robbed). Since dome ports are just too damned bulky, what I typically carry-on is: macro port (and extension ring), 100mm macro lens, 50mm macro lens, at least one strobe with cords, and the housing (with camera inside). I then pack everything else (2nd strobe, wide angle lenses and dome port, etc.) in my checked bags.
BTW, I too have gotten rid of all my Pelican cases and opted for bags that do not scream "Camera Gear Inside!" For example: No camera gear here!
Anyway, part of my reasoning is that I at least want a macro lens, together with a mid-range lens (for my full frame camera, the Sigma 50mm macro lens is perfect for the latter; for cropped sensors, I'd probably take a mid-range prime like a 35mm) that can be used for fish and reef shots without a dome port. Such lenses are not terribly expensive, take up very little space, and would work really well as all-purpose lenses if your dome port and wide angle stuff was all lost/stolen en route. Frankly, some of my better photos (schools of barracuda, individual fish, etc.) have been taken with that Sigma 50mm lens (two of the photos on the Inon "Featured Artist" page here were shot with it).
The point is to take just enough stuff in carry-ons that -- in a pinch -- you could shoot macro, fish, and some reef shots the entire trip with just that gear, and the trip would not be a waste. I still pray that my checked bags will reach the destination intact just like everybody else does, but if they ever don't, I'll still have something to do...