I did an experiment with a pass-like password manager, to get around the filenames issues :

Basically add an entry named "index", containing all your entries names. Then, using a wrapper, hash the password filename with sha256, and store it under the hash, not its own name. When you need to query a password, retrieve the "index" entry which lists the actual names, select one, hash it and query the hash.

Using this technique, your password list is encrypted too, and you need access to the store itself to know it's content. Also, you might want to salt your entries names (you can use your gpg key for that for example when using pass(1))