So I am having trouble getting apps to show up in Desktop search or the Desktop menu. I can only access them from terminal. How can I have them automatically added to the desktop menu? 
What distro is this and what shell do you you? For completeness, can you do echo $XDG_DATA_DIRS in a terminal?
Normally, this variable should include /var/lib/snapd/desktop/applications, which is added by /etc/profile.d/snapd.sh.