Jake: "Protective clothing for beekeepers would also be a good idea. Maybe leather armour..."
Leather (cow) has one of those smells that can really agitate the little devils; also bananas (these are things you learn).
DFWiki: "The royal jelly is a counted as an edible item and can be cooked or eaten as is. The honeycomb requires a
bit more effort, in that it must be brought to a screw press..."
Honeycomb is an edible item too (eaten wax and all). It comes ready-to-eat straight from the hive (once you get the bees off). Seperating the honey is good for storage because some bugs like to eat the pollen embedded in the wax and can mess up your honeycomb. Of course you could also keep your honeycomb safely preserved in honey

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DFWiki: "Once the artificial hive is built, it can be set to either allow collection of hive products (which destroys
the hive)..."
That's sad. Don't use skeps little dwarves! You don't need to kill your bees to get honey and wax. Also, hives are hard to kill without using poison (skeps were usually harvested/killed with sulphur fumes). Top-bars are a better option.