Yes but in a proper hive we are only taking their excess storage. Normally they are chill enough that you don't have to smoke them for it unless it's the end of season and they want it for winter.

If the farmer doesn't clip the queen's wings, they can just fly away if they don't like the nest conditions

Honey bees can recognize the beekeeper's face and decide not to sting him, so I guess they're somewhat cool with it: https://cals.ncsu.edu/news/can-bees-recognize-faces/

Bentham's Bulldog makes the argument that not only does harvesting their honey cause major suffering to bees, it's actually the least ethical thing to consume in existence. https://benthams.substack.com/p/dont-eat-honey

I'm unsure about it either way, but it's worth reading the argument IMO.

Some bee keepers feed them sugar if they think the hive will need it.