Center negative DC plugs are used because that way the switched element is +ve not gnd. Don't want to be switching ground references when you are using audio or music gear, so they make the center pin negative.
I always thought it made perfect sense.
What's the relation between where a wire is sitting, and a wire that is switched?
All of the commonly available DC jacks switch the barrel, not the center pin, and we use that switch to disconnect battery +. Also, in effects pedals anyway, the way the battery is switched on is a stereo jack is used, and battery ground goes to the inner tip of the stereo jack. When you plug in a mono 1/4" plug, it connects the inner tip to the sleeve and makes the ground. So all of this adds up to generally having center negative plugs. That's how Boss started doing it decades ago, and now it's pretty much THE standard everyone uses unless you absolutely have to do something else.
Like I said before, though, in practice, it's a non issue. The transformer isolates the plug, so it's actually quite difficult to cause a problem unless you're really trying. Even power supplies with multiple outputs are generally isolated these days, all but the cheapest solutions, but even if you short to the case with non-isolated multiple outputs, even the cheap power supplies generally have some sort of crowbar protection and just shut off.
Anyhow, that's the history of why it's the way it is. 30 years ago, someone came up with a solution that worked very well with commonly available parts, and everyone quickly standardized on that solution. There was actually a little fight for a while. I still have a couple of old effects here that are expecting something like 1/8" phono plug for power. Now THAT was easy to short out if it was just laying around, and it disappeared right quick.