There it is, related to all the other errors (beside first).
Found that one, where solution was to remove apps.json from oc_filecache database table, if the file is really not there: App Store not working anymore - #5 by bastoGrande
I guess since everything else is working as you say, access permission will not be the problem.
Do of course a database dump, at least from oc_filecache, put nextcloud into maintenance mode and then in mysql it would be delete from oc_filecache where name='apps.json'; to delete all entries with that filename.
select * from oc_filecache where name='apps.json'; is good to find the right entry first, also because you have two instances and only want to delete the entry for one of them.