The last part is not quite right, but the interesting question is how we should correct it.
"Well, the queen and worker bees are all females. It's the drones who are all males." (It's better as two sentences)
Can we correct the last sentence as "They're the drones ..." as you mentioned?
No, we can't. "they" normally refer to something that has already appeared, so what is it referring to here?
It can't be "the queen and worker bees" since they are not males, and it can't mean the carpenter bees either.
What's left is the drone bees, but it will make the sentence "The drone bees are the drones ...", which makes no sense.
I believe what the speaker meant is: It's the drones THAT are all males.
This is a common "it ... that" emphatic sentence pattern. "It" is just a placeholder that has no meaning.
You can use it whenever you need to emphasize a specific part of a sentence.
For example:
- Money matters => It's money that matters" (title of an old song)
- I love your honest above all => It is your honesty that I love above all.
- I do this with a great pleasure => It is with a great pleasure that I do this.
The speaker meant "Drones are all males", but since he wanted to contrast them against the queens and workers, he employed the emphatic pattern, but made a mistake doing that. The "it ... that" pattern doesn't allow other pronouns in place of "that" as far as I know.
Note that there are sentences that might appear like the emphatic pattern but actually are not.
E.g. It's the Smiths, who are our neighbors! (the speaker has just spotted them)
The "it" here is not a placeholder but a pronoun referring to "what I see in front of me", and the phrase is not the emphatic pattern but a relative pronoun compound sentence. "who are ..." just modifies "the Smiths", with no special emphasis.