Beekeepers who produce queens for sale breed them for various attributes, such as mite resistance, gentleness, and productivity (of honey). The queens that they use for the first stage (for making the eggs that will be grafted) are quite valuable. Though it's still not worth stealing unless you can set up a similar operation, which means there wouldn't be very many suspects.

(There are also beekeepers who artificially mate queens to better control for male genetics. That is a very labor-intensive process, and those queens are correspondingly more expensive, but the main queens probably aren't any more valuable than in the process I described above.)