Spatz
Egahds, I've been gone a long while!
I think they'll still make appearances. I doubt they'll have killed them off. They just might not be doing gymstuff anymore, what with their towns frozen over.
Though this does raise an interesting question. If these new gyms were always present, how did they fit into the League? Were they always proper gyms, or are they de-facto gyms to replace the ones that got frozen over? And if they were proper gyms, were their badges valid? Is it that getting any eight badges would get you into the League? Just food for thought.
Simple: badges are available at all gyms, including ones not normally seen in games. I believe in the provided link, Trips Badges best define this, as he has three that Ash does not, and thus suggests the possibility that he has acquired the two of them from the new gym leaders. (All speculation of course, but...)