I don't believe you can truly make the bike inoperable. Yes, you can make its electronics inoperable but I don't believe you can feasibly make its battery, engine or the mechanics inoperable.
I mean theoretically you could, but not in a safe way.
Bike thieves aren't bike mechanics and modern hardware has chips that could fail to perform their task or even brick themselves. It could fail to charge or stop charging at 10% it could spin up the motor but inadequately. It could appear to start but gradually turn off for no reason 10 minutes later leaving it in all instances a safe expensive human powered bike.
It could broadcast I'm a stolen bike with cords with the electrical pathway to the transmitter being also wired to something else more vital.
You could pass an encoded unique to device signal over the rest of the system with chips elsewhere expecting that signal and noping out if they don't get it to foil rewiring.
You could require a periodic modifier received over the air encoded in chip2 .. chip n but not available in chip 1 like a series of codes for your key fob to unlock your car.
You could absolutely make it as hard to defeat as defusing a bomb and lunatics who wave glass bottles are no longer stealing your bikes.
I'd rather build a much simpler bike with the parts - the chip won't do a thing. Heck even the battery pack and the brushless motor + the frame are fine on their right own.
Which suggests locking it at the battery level might more most profitable. Looks like they cost as much as $900. Crackhead thieves that wave around broken bottles aren't going to be highly inspired to buy a new $900 part to render their $2000 bike that they intend to sell for $1500 serviceable.
It takes a one step $1500 profit to a 2 step $600 profit. Might as well rip off the best buy for crack money instead.
Those batteries are vastly overpriced. The individual cells cost next to nothing and the BMS in them is an off-the-shelf component. But almost all of them contain some kind of DRM which makes it so that they only talk to their own manufacturers motor. This makes repairing them a fairly difficult thing, especially because they are typically constructed in such a way that opening them up is hard or will break stuff.
Triggering inoperability in a safe way is not an issue.
The problem is that you would need to reach mass adoption of the technology, so that the fact of that specific item not being worth stealing would become common knowledge.
I mean theoretically you could, but not in a safe way.