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I have files that are owned by me, but can be only accessed through a search. Once I find the file, it shows me the directory that it is supposed to be in, but it is no where in "My Drive". I can right-click and "Add to My Drive", but the file is owned by me!
Why are there directories that are hidden that will only come up through a search? Why can't I see them in "My Drive"?
It sounds like you have found what Drive refers to as missing or orphaned files. This happens when a Drive file loses all of it's parent folders. It still exists, but it's no longer accessible in My Drive or by navigating your folders.
To find all of these "orphan" files open the Drive web UI and In the search field, type: is:unorganized owner:me. Source: How do I find missing/orphaned Drive files?
As you mentioned in your question, you can now add them to My Drive to fix their orphan status.
