You can’t shuffle a bag or a deck of card by hovering the mouse over them and hitting “R” on your keyboard if they are locked, but you can right click -> shuffle on them and it works.
I think the current behaviour is inconsistent. Either an object is not modifiable and then no way should be allowed to alter it, or both way - mouse menu and keyboard shortcut - should work.
I think this is a design “error” and should be rethought. This is very likely also related to https://tabletopsimulator.nolt.io/2118