Been there.
First: keep in mind the omnipresent struggle of time against space (in computer science processing time against memory requirements)
You said that want to keep minimum information possible at first (space), and next talked about some temporary matrix reflecting the quartenions, which is more of a time worry.
If you accept a tip, I would go for the matrices. They are generally performance wise standard for 3D graphics and it's size becomes easily irrelevant next to the object data itself.
Just to have and idea: in most GPUs transforming an vector for the identity (no change) is actually faster then checking if it needs transformation and then doing nothing.
As for engines, I can't think of one that does not apply the transformations for every vertex every frame. Even if the objects keep in place, they position has to go through projection and view matrices.
(does this answer? Maybe I got you wrong)