That’s part of the appeal. It allows for sandboxing each password to its own vault essentially (you pay a privacy cost, which I don’t mind anyways, and my disk is encrypted).
Gopass does encrypt file names too.
I don't think this is that big of a deal though.
Also, I don't know if other people do this, but I don't actually use the pass scripts, and instead have my own scripts for managing things that just happens to be very similar to pass. I extend it in whatever ways I want to.
If I cared about this issue I would probably consider putting the passwords in a file system on a loopback mounted luks volume backed by a regular file, or maybe just store them in a different format altogether.
I do realize that the average user doesn't want to bother with all of this and wants something that "just works".
Only if you disregard that pass doesn't encrypt file names.