Yes, if you take as your only example one of the lowest-quality applications written in the java language, and make an elementary logical error ("this is slow, and it is modular, therefore all modular things are slow" - this is an example of the classic "all men are socrates" logical proof), then it is perfectly reasonable to think that everything it does is inherently slow / buggy / etc.
Actually, OOP is not that bad, and neither is modularity, unless it is overdone. Without modules, one would have to program the whole app in one chunk, which would be kind of bummer, to say the least

. Without classes, development would be relatively slow

.
I guess what I'm trying to say is that
(1) I am not a C programmer

(2) modularity at the OOP level is fine -- loading classes doesn't annoy me too much, it's an acceptable "waste" given the development time saved
No more comments on NB :-/
Regarding the original topic:
A u3d loader that supports all kinds of graphics would probably not be too efficient. Personally, I would prefer not to go the "all-encompassing .u3d file" route but rather do something like ".u3d with specialized, optimized loaders for specific kinds of models".