A shower that drains into the bilge is easily fixed with a blivet on the end of the drain hose, or installing a shower pan and sump.
Heat coming in big glass windows, also fixed easily by applying 3M Crystalline or similar window film, which can cut something like 98% of all IR radiation through the glass, with or without any extra visible tint. Great stuff.
But a Nauticat is what it is, no matter what you do to it. Gobs of room, up and down, for the length. Which will mean gobs of windage and motion, as it will on any boat. My impression is that they're really built as comfortable harbor boats which also can conveniently transport themselves under engine or sail, but they're designed for the destination and not the journey.
Of course a single-level more conventional design is going to mean either less accommodation space, or a steeper marina bill for the extra length. But I think if I were crossing the Pacific and the Equator, and then circumnavigating Oz, I'd want a more conventional cruising boat aimed at the best experience (comfort, safety, speed) at sea, rather than one built for comfort in harbor.
The Nauticat 38 - information for cruising sailors
Says capsize ratio 1.51, fwiw.