Is it dangerous or unhygienic to deshell an egg over the bin?

Not aware of anything in the handbook specifically. But the intent and spirit of the handbook is important. While what you've done isn't a kitchen crime. I'd be proud to go to, or work in a kitchen that is this pedantic about safety. here are some points to think of:

Generally you want to treat the vicinity of the bin as a one way. Food goes to the bin and doesn't comeback.

One issue might be that if you lose the egg, you can't recover and the optics of it is not good.

The other problem is that you know there is bacteria in the bin and long past the food safety safe zone. Why hang out there with food to be served and with eggs which bacteria love.

Presumably you're standing over the bin and there may be splashback, shrapnel, or other spoilage making into your apron/hands etc.

Part of Mise en Place is a clean set up and what you describe isn't exactly Mise en Place.

I agree with Mando. If something seems unhygenic or disorganised then it's best to avoid in the spirit of well run kitchen even if the science isn't there to back it. The idea of a one way direction for waste food is pretty key to not mixing foods.

The most dangerous bacteria in the kitchen are on the uncooked meat and surfaces that they come into contact with rather than some 'gas carried bacteria' which would be carried through the whole kitchen each time the bin pedal is pushed.