I am using Krusader compiled from master (2.5.1-beta, revision 5056272) on Ubuntu 16.04. Both the main Krusader window and Lister show their main menu bar both on top of the screen (where it belongs) and inside the window. This was working correctly with Krusader 2.4.0-beta3. appmenu-qt5 package is installed and working correctly from what I understand. konsole and kate applications are also affected, they allow hiding the in-window menu however - the former via menu, the later only via Ctrl+M keyboard shortcut. Krusader has no such functionality.
I assume that the issue here is https://bugreports.qt.io/browse/QTBUG-54793 - it's supposed to be resolved in Qt 5.7.1, yet what I have installed is Qt 5.5.1. Qt 5.7.1 on the other hand won't be available before Ubuntu 17.04.
After updating to Ubuntu 16.10 (meaning Qt 5.6.1) this issue is gone. Not sure whether it is still worth investigating then.