I do not think the NIH syndrome is by any means limited to the DXSDK team but more a general issue with any sort of developer :)
NIH syndrome is a symptom of poor culture and poor management, not of poor programmers.
Regarding not using .X files to "protect" your assets, that's totally worthless. Any asset encryption system you can think of will be broken, if your game is good enough that people want to mod it. And anyone who wants to rip art can easily just snarf it straight out of the Direct3D command stream using DLL injection. The protection you have against art theft is the laws of the land, not any particular technical trick.
The best reason to not use .X for a game would be if you needed a feature it didn't support (LOD and morphs are hard to do in .X), or if the cost of loading and processing the mesh was too much, and you needed a "memory ready" mesh format.