There are certainly cases where NX works better than VNC: Say, with well-behaved applications on very slow connections.
Oh, come on. The only instance in which VNC *might* outperform NX is on a LAN. And my bet would still be on NX there. We used RealVNC and then TightVNC over T1 connections for some months and we found them to be quite unacceptable for performance, and even worse (far worse) for display quality. This is for general business desktop use. Web, email, OO.o, lots of PDF viewing, often parts manuals with lots of scanned images. Some IE under Wine (unfortunately). We throw a lot at our remote displays and NX shines where VNC chokes. The mini-eval I just ran on TigerVNC reported 2047kb. It was better than when we used VNC several years ago. The video quality was good, as it immediately selected a sufficient color depth. But the performance was markedly inferior to a side by side NX session.
Regarding well vs poorly behaved apps... if there is an app that chokes NX but not VNC, I have yet to see it. Tiger/Turbo may, indeed, do well on 3D over a LAN. But my business desktop clients have generally opted against providing Doom 3 to the thin clients. Out of curiosity, what customers do you have who are interested in FPS, and what are they doing?