Difficult to thieve idea - shorting the motor.

I just had a thought... as you do.

In my electric bike build, I used a three way XT-60 style connection to the three phase hub motor, to replace the crappy bullet connectors originally supplied.
I can't think of a good reason not to build a shorting plug to go in place of the phase wires coming from the controller, this would effectively make the rear wheel a brake. If you left the bike unattended, and disconnected the controller and inserted the plug, even if theft was attempted by riding away with no power, the rear wheel would literally be a drag?
It certainly doesn't forgo standard anti-theft measures, but worth a go, I can't see any technical reasons not to try it.

Should do the job. Some controllers actually have a similar function built in, called anti theft or something.

It's been done a number of times over the years, with plugs and with switches and relays and with active electronics (like the "antitheft" option in some controllers), etc.

A plug is safer for you than the switches or relays, because the latter two have the possibility of a contact switching failure either during switching or under vibration while riding. Under the worst-case such failure, the controller can be shorted out (which on most cheap controllers will blow the FETs).

A plug can't do that cuz you'd be unplugging the controller first, then plugging in the shortng plug.

It would definitely slow down anybody trying to move the bike

You just need to make sure there's no way to have the motor shorted when the power is applied. Unplugging the controller would be one way, but sort of a pain. Another way would be to use a hidden switch that both shorts the motor and disables the power to the controller.