Link2SD does not link application's private data files that are located in /data/data directory, they remain in the internal storage. Thus each app you install will still have some data on the internal storage so you can still potentially fill up your internal storage even if you are moving all of your apps over.
I wish to ask this before I go bothering the application author. I figure there is some well-known issue here which I am not aware of.
I may have to switch linking apps because my /data part is getting too full, mostly due to Google's crappy maps and browser apps, which are horrifically fat.