Hello,
in order to answer you i have created a subfolder and looked at the maildir directory.
if you create these folder:
test
test.sub
postfix(in my case) creates both directories at the same level. That tells me that for postfix they are independent folders (maybe i am wrong).
When you tell roundcube to delete test the maildir directory test is deleted but not test.sub.
so unless roundcube is modified to delete all folders which name start with test. then they won´t be deleted.
I hope this helps.
Ed.