do your plugins need to worry about the split of geany.conf and session.conf?
No. But the same issues affect Geany. Geany is worse in some ways because different systems are used in different places.
As @kugel- sagely points out, lots of Geany prefs don't use stash, either because it wasn't invented when they were added, the person who added them didn't understand stash, or they needed something too complicated for stash (like variable numbers of entries or variable key values).
Preferences can be migrated. Stash can be extended.