Many of them will be, or the functionality will be incorporated into the core. I don’t think OAI-PMH Harvester is on the short- or long-term plans right now, though. The list you cite is the best guide.
Theming (like everything else) will work on a very different system, so your custom theme would need to be rewritten.
Omeka Classic and Omeka S will both continue to exist alongside each other for the foreseeable future.