Currently /usr/share/applications/emacsclient.desktop opens a file in a terminal. It makes more sense to open it in a new window frame. Please, add the "-c" option to emacsclient in the Exec line of the emacsclient desktop file.
We simply stick to the upstream default, which is to reuse the current Emacs frame. (Which is not necessarily in a terminal, but could be an X frame too.)