Why is my migration status table empty?
I think that you are mixing up things. By doing

drush config-delete migrate_plus.migration.ID


you are just deleting migration_plus configuration but you are not disabling the module, it is still enabled. If you really want to disable the module and of course the configuration, you'll have to drush pm migrate_plus.

Concerning the "No migrations found" message, your custom module has to define correctly the new migrations (.yml files).