I imported from keepass way back when I was getting started, and then never really went back to tidy. So either as a constraint of keepass or a self-imposed rule I had when using it (I don't remember) everything is within a directory; no top-level passwords. There are some redundant paths, like `internet/` and `forums/` but I generally make heavy use of `pass search` and try to make sure the actual filenames are properly descriptive (usually of the URL), and then don't worry too much about the path. I do actively do upkeep on trying my best to make paths and filenames unique at the second character, so that I can access commonly used ones quickly by typing two characters, hitting tab, and repeating until done.
I have a habit of going in to edit a file before replacing an old password, and duplicating the top line onto the second line, which allows me to access the old password for a while with a lot more ease than mucking with git.
For things like computers, I overload the path a little. The computer name is the .gpg of the most often used account, and also a directory with the other accounts within. That way I can:
pass /lan/nas # access my personal user
pass /lan/nas/www # access other accounts