Is it possible to add folders in config/install?
No, you can't put config in sub-folders, those are reserved for config collections (e.g. language overrides/translations).

The only option would be submodules as you already said, and it's up to you to decide if that's something that makes sense for you.


  For some background, I wrote a Python daemon that does server monitoring, and the module handles communication between the monitors and a central reporting server. Each content type corresponds to a plugin for the monitor, so someone could turn on only the plugins that they want.


Not sure I fully understand that and it's not exactly the same but our project https://www.drupal.org/project/monitoring might still be interesting? it uses plugins and a single config entity for a sensor, it is about monitoring things about a single drupal site and not other servers (We do then use sensu to collect the data and alerting).

And without having the full picture, using content types/content for something that doesn't really sound like content seems like a strange idea. In Drupal 8, it's pretty easy to create your own entity type with support for bundles, then you could make all the shared fields base fields and would probably get rid of 90% of your configuration.