The only problem I got with the password store application is that the Git integration seem to be a bit broken.
It often refuse to push, pull or sync depsite having no conflict.
But you just have to delete the store and pull everything again, so it's not a huge problem.
I don't think the git integration can be broken. You can go into the ~/.password-store directory yourself and see what is going on next time you have issues (it's just a regular git repo).
I definitly have to try the yubikey integration !