I think you have a point Clive - but from what I can tell Universities still have paper copies... well in astronomy I know this to be the case. I read most of my papers online but the Uni has to have a subscription and as part of that their library has paper copies of each issue. Now in terms of online only ones - I see an issue, indeed - unless we just maintain digital libraries forever... which of course isn't guaranteed. There is a resistance to this type of publishing in astronomy and I see the big journals out-lasting these upstarts, assuming they change their online model, thus there will still be paper copies. I think Astronomy has this quite nicely. The journals take you paper and put it only and print out, but don't stop you put their non-editted version on arxiv, which is a free public paper database, thus there are slight differences but everyone can see all the work going on without much hassle - and if worried the paper search engines even allow you to retrieve the public version, or the one from the paid journal.
I guess I see an issue, but not if they are smart.