I’m running 18.04 prerelease and have installed some snaps such as PyCharm and Gogland. Their icons showed in the applications list to begin with, but have recently disappeared (I’m not sure if after an update or what).
I can’t find any .desktop files in ~/.local anymore.
Snapd doesn’t install the .desktop files into your home directory. Installed snaps’ .desktop files are located at /var/lib/snapd/desktop/applications/. That said, sometimes logging-out and back-in restores missing icons in the overlay, and other times if you’re currently running in a Wayland session then logging out and then into an Xorg session and then back to Wayland might restore them.
I just checked the bug tracker and it seems we don’t yet have it listed, even though it’s a known issue. It would be really helpful if you could file a bug for it at https://bugs.launchpad.net/snapd