the biggest problem is when you touch all the pins with your finger trying to find the socket when plugging the joystick in.
No, unless your finger's wet, or you've had it in your nose or ear. The biggest problem is when you fumble around trying to plug in a metal rimmed plug (like some mouse plugs) and the rim shorts pin 7 to the joystick port skirt. Apart from that you can plug and unplug a plastic joystick plug while the Amiga is on without any danger to it.
The biggest anoyance is the recessed joystick ports, you cant see them unless you have a go go gadget neck.
BTW. If you had a special joystick made up it could be detected by providing a resistance on pin 5, the lightpen button / X-Pot connection. But normal digital joysticks; no go on a detection there.