For ports of mouse-centric PC games, I'd imagine the most optimal way to play them would be in tabletop mode, with only one Joy-Con corresponding to your dominant hand detached and in mouse mode, while your second hand is used for the touchscreen to access things you'd use hotkeys for on a PC.
Real-time strategy games are constantly being used as an example of a genre that can benefit from this, so using Starcraft II's HUD for example:
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See all those buttons that have letters/numbers showing what key you can press to use them? You'd be using your free hand to press them while your mouse hand is used for selecting units and telling them where to go. (hopefully in this hypothetical SCII port that utilizes the touch screen+mouse joycons, they'd let you move the command card on the right to be next to the radar or vice-versa for lefties)