You can hotplug them, but when plugging them, there's no short risk, as all pins have their individual connectors. A barrel TRRS headphone connector can short, because the first "pin", the tip, goes through every single connector. Imagine this was power, and one of the connectors it went through was ground.
The stock GC controller ports place the contacts next to each other, rather than at different depths, so they won't connect controller pins to the wrong port pins or short pins together when partially plugged. (I do suspect the ground and/or power pins may be longer than data lines, to connect first.)