Yes OCIS (owncloud infinity scale, a complete rewrite of the owncloud project) has a convoluted file structure and I guess OpenCloud has the same way of storing files.
This is the main drawback I see as well, but it isn't a deal breaker for me. The way they handle the files allows OCIS and friends to work without a DB, in a stateless way I guess? This means that the entire setup is fully deterministically defined from a single file. This makes rollback very easy. So my rationale is that the files remain accessible even if a particular version decides to implode.
Thanks for pointing that out!
https://owncloud.dev/ocis/storage/storagedrivers/