Do you mean that shake can't read a .iff file that have motion vector, or that shake discards the motion vector part of the file?
Shake seems to understand a .iff file with motion vector. Unless shake discards the info, it could be possible to access the info from within shake.
The shake support didn't told me if it could be done, but told me that they won't do it because not enough people request it.
Bottom line if you want this feature to appear in shake, please suggest it. If they have enough people asking for it, they will implement it in futur release.