I don't think this is about making the Vorlons harder at all. I think this is about giving the list a bit more variety so that it's not always the same ships turning up. If carriers and scouts are out, what about other ships, something to give them some variety?
From what I've been told, e2 playtesters did examine the scout question in depth and I'm sure the same was done for the carrier. Is there any chance that someone can pin Mathew down long enough to get a detailed reason why neither made it into the list?