If I end up using a Dual Schock 4 or a Dual Sense when my Steam Deck is docked, will I have to pair them again with my consoles every time after using them with the Deck?

Just get another used gamepad used if it becomes an issue! That is the beauty of using a computer instead of a console, most gamepads are going to work and with Steam’s controller interface it is easy to select a control scheme that will work well for that controller.