See attached code HelloMnemonic.java
The menu bar has two entries and in each one there's an item which is bound to a shortcut defined with a letter + Ctrl + Alt:
Menubar > File > Open : bound to Ctrl + Alt + A
Menubar > Edit > Copy : bound to Ctrl + Alt + C
 
All described below occurs the same with a simpler shortcut such as Ctrl + A.
I run it and issue one time each of the two shortcuts; what gets printed is:

menuitem1 got Event: javafx.event.ActionEvent[source=javafx.scene.control.MenuItem@28bb494b]
menuitem7 got Event: javafx.event.ActionEvent[source=javafx.scene.control.MenuItem@58df0438]

This is perfect each action associated to the menu item is called one time.

Now I modifiy a little the code to move the Edit menu so that it becomes a sub menu of File (attached HelloMnemonicModified.java).
We now have:
Menubar > File > Open : bound to Ctrl + Alt + A
Menubar > File > Edit > Copy : bound to Ctrl + Alt + C

I run it and issue one time each of the two shortcuts; what gets printed is:
menuitem1 got Event: javafx.event.ActionEvent[source=javafx.scene.control.MenuItem@298488ef]

The action attached to menuitem7 is no longer called.