I haven't messed with the nif optimization in quite a while but last I remembered you weren't supposed to optimize player meshes, creatures, armor, clothing, things like that. Basically anything with an associated .egm file should be skipped.
Go to tesnexus.com and search for pyffi and read up on the process there.
I looked it up but there's no real info on it... just a bunch of people confused like I am. I'm not sure that I see any egm files in the data folder either. I'll keep looking.
I'm guessing by the lack of responses... that it's not a very popular optimization. So it might not be worth even doing....