I'm no Nauticat expert, but have become obsessed by these wonderful boats. I've also not been on the NC42 pilothouse, but have been on the NC44 Traditional Motorsailer. Additionally, I've been in contact through the years with various owners of both. They are different yachts intended for different tastes and personal preferences.
The NC44 is actually a larger version of my boat, in most respects. It is a ketch with a full keel. Ours is proportionally a taller rig than the 44, has the modified full keel and a skeg-hung rudder - a cross between fin keel and full. The sails on the NC44 are relatively smaller than the NC42, being a ketch rig, so the boat's easy to single hand - with less stress on an older couple as well. The boat's a very comfortable hybrid, capable of motoring or motorsailing at speeds exceeding 10 knots . . . can't testify to the sailing performance of the NC44, but ours is a pretty decent sailor.
Our NC33 also has fuel tanks which hold 160 gallons and a 140 gal fresh water tank - enabling long passages without refilling. She tracks exceptionally well and is stable under all points of sail. I'm certain the NC44 has even larger tanks.
Here's a smaller scale drawing of my NC33 - as a comparison:
There are various interior plans to suit different needs - family or liveaboard couple.
SD's comment re: side doors being problematic in heavy weather is not entirely true. We have port/starboard sliding doors with wide side decks. Regardless of what tack we're sailing on, we can always safely egress the pilothouse and cabin interiors on the high side. I actually prefer not having a companionway off the aft cockpit/helm - creates more room for seating and less disruptive traffic.
This is the Nauticat most preferred by liveaboards who want to cruise comfortably and safely, with minimal efforts.
The NC42 Pilothouse is a sloop, designed to provide for improved sailing performance. As I said, I haven't been on one, but do like the lines and overall concept over the more traditional motorsailer.
If you haven't already done so, check out the Nauticat web site