I'm not sure when my top menu disappeared, but I decided to look into this today. I think the issue may be an Electron / Wayland problem. I'm running Garuda Linux (Arch based) using KDE and the latest Joplin appimage. The menu is not showing, but if I run an X11 session it is there. I tried some of the command line fixes that previously worked and I could sometimes get the menu to show under Wayland but those command line parameters caused the program to not start at all unless I did it from a terminal. Even then launching the program failed most of the time. And if it did run, I could only run it again by logging out and in again. It's a mess!
In the end I just decided to continue on without the menu. If I need to configure something or use a feature only found in the menu, I'll have to log into an X11 session.
I assume that when using the appimage the correct version of Electron is bundled into the image. Is that true? If so, I know the newer versions of Electron are Wayland by default. Either way, I don't believe this is a Joplin issue.
I went ahead and filed a bug report. I was able to use the developer tools panel and verify that the Joplin appimage bundles it's own version of Electron. Maybe the developer has some control over the issue?