Yup, if combined
all folder windows would look like a stack of cards with no label. If a subfolder is opened it will be grouped
with the parent folder as CJ said. The taskbar icons will move together.
You can't choose specific folders not to show the navigation pane, that option will apply the setting to all Explorer windows.
I suppose you have a reason for 3 folders with program shortcuts. Would it not be faster to pin
those shortcuts to the Start Menu or even the Taskbar? Should be the same amount of clicks.