In general, I think including a link to documents (as opposed to embedding the document in the database) should have a negligible effect on sync. I don't do much file linking in my OmniFocus database, so I'll let folks better equipped to speak from experience respond. :-)
I did want to say that it's our
intention that sync should work indefinitely, assuming that the tips posted at the start of
this thread are put to use. (Regularly move completed stuff to the archive, for example, instead of letting years of completed actions accumulate.)
And, if folks do end up having trouble, we're always happy to help!