Are you sure, the elements are actually vectors? If so, OpenGL might be the issue here and you may have to turn it off. If not, then it is reasonable to assume that in fact the AI file just contains a bitmap and then for logical reasons AE cannot do anything it couldn't with any other layer based on pixel images.
Certain effects applied to layers in Illustrator can cause the vector data to rasterize in AE. EPS files may also rasterize so collapse transformations has no real effect. A little more detail about your vector files would be helpful. It would be especially helpful if you would post the file.