I'll tell you what I know...which isn't much. I'm not a programmer, and I'm not sure what encryption process the models/levels went through.
Basically, the in-game models were created using the same process as Jedi Knight. We have .3DOs, .MATs and .KEYs just like JK does; we only did a few mods to it. However, instead of having separate files, we compiled all the information into a single file for each model, called a .BAF file. We also included additional information regarding scale, palettes, weapon nodes etc. etc. So, I don't know if any enterprising hackers out there have tried to 'look' at the .BAF files, but if it looks like a .3DO, it probably is
I know that doesn't help any non-hackers out there. The short answer is 'no', the long answer is 'maybe, if you spend a lotta time breaking your User Agreement and hacking into the files.'