This is a sure way to blow out the CIA chips in any Amiga model. If you haven't, you one of the luckiest people around!
That is indeed a really huge design flaw then. Like i said, alot of games force you to swap mouse with a joystick during the game, due to the fact that you need a mouse to start the game.
But this thing just cannot be common, as all my friends did the same and i see no easy way of shortcutting any of the pins using a standard amiga joystick or mouse, unless you are extreme unlucky. So i beg to differ.. It is you who were extreme unlucky if that happened.
I dont know of a single person who have blown their amiga this way. I know however of one who killed his a2000 by connecting a floppy drive while the amiga was powered on.