Tried SSH'ing into a Linux machine with the same user that was also running a the gpg-agent daemon. I tried to decrypt a file with the basic "gpg -d ~/filename". This output info about the file and then just hung. No password prompt at all. If you do this via a GUI term on the same machine you get a pop-up box with a password prompt. Seems like the gpg-agent is taking this request, and not presenting anything back to the same user SSH'ed into the machine. Had to find a way around this.
I finally found some posts on the net with people having the exact same problem. The gpg pinentry mode "loopback" fakes a pinentry by using inquiries back to the caller to ask for a passphrase. Buy doing this with the command "gpg -d --pinentry-mode=loopback ~/filename". This will get you back your password prompt, and allow you to decode the file remotely over SSH.