I still don't understand why you move from your photoshop application to illustrator.
your main compositing application should be the one you got the files in.
if thats photoshop then do all your work in photoshop
if its illustrator than you should do all your work there.
you can scale your SVO indefinitely while in photoshop (if they are vectors to begin with of course)
you don't need to go back to illustrator to do so.
if you created them in photoshop than they could of course could only scale at the maximum scale you created them in.
and they will open as a seperate psb file.
basically the approach when working with multiple psd elements is you work with two files:
one is your design file -> the one you got from the designer
this file is the one you show to your client and make design changes too
since this work is done for you now, you can now duplicate that file and make an AE copy
where only the necessary files are there, merge what you can to avoid the clutter.
in this file you:
1.name good understandable names for all the layers
2. apply all pixel masks because you dont need them anymore. you want the file at their true cropped size for ae.
3. you can leave smart objects intact or rasterize them (it doesn't matter) but you scale them first as you wish to the largest size needed for ae.
they will be imported to ae at cropped size (if you choose that when you import) as pixel layers
4. delete duplicated elements that you intend to animate in AE so you wont make the same animation twice (D.R.Y workflow)
5.consider that clipping masks will import as precomps with their clipped contant so merge what you can to avoid moving between precomps
6. merge what you can. if there is no need for those elements to move separately -> you can merge them.
see if that helps and if there are more questions ask away.