@jk the only way I have found that works is to repeatedly use the shortcut instead of clicking. It means you look it up (open the menu / find the entry in a command palette), then use the shortcut to perform the function (even though that slows you down at that point!) , until you don't need to look it up anymore.
I might say I "know" shortcuts primarily as something like muscle memory, not as a fact. That part of me doesn't seem to need things to make sense.