I'm making the same comparison except for a D7000 housing. I reckon there're both top notch housings, and would be happy with either. I've been doing a lot emailing, internet research, asking people I know who use both systems, and so forth.
It turns out to be a myth Hugy are super $$$$. They're about on par with other major manufacturers. In fact for what I need a Hugy system is cheaper than the equivalent Nauticam, and I'm able to get a Nauticam system for a good price (much less than what the official local Oz distributer has quoted me). The housing is marginally cheaper and odds and ends such as gears, extensions, ports, viewfinders are a bit cheaper too. It all adds up.
What I like about the Nauticam is there are four places to attach mounting balls. You can have your strobe arms attached to the handles or atop the housing, then use the other two for focus lights or whatever. However if you add a right side handle to the Hugy, you have three mounting balls, which is enough for me. Also Nauticam make a zoom gear for the Tokina 10-17mm + x1.4 Kenko TC combo, and Hugy don't.
I also looked into the mini fisheye dome options and initially it appeared Hugy came up short, which would have been a deal breaker for me. However a Subal mount Zen works with an adpater, and Zen are currently developing a Hugy mount for their domes, due around late Feb 2011. Also Hugy advised they are looking at making an acrylic mini fisheye dome of their own.
I really like the Hugycheck system too. To confirm 100% pre-dive your expensive gear is waterproof, is awesome. Also I reckon that neoprene strap would be good for one handed vertical shots, as the housing would just hang off your right hand.
So weighing up all of the above I'm more or less decided on a Hugy. Now to shell out the biccies!
Cheers,
Dave.