Yeah, the Queen bee stores the genetic info from both the princess and the drone, but the Beealyzer will only display the Princess's characteristics, and the imprinter will only modify the princess's characteristics, leaving the drone's untouched. That's why, after the Queen dies, some (if not most) of the offspring will have the original drone's unmodified traits.
I had thought that the Gendustry imprinter would change the traits of both parents, when used on a queen bee, but evidently that is not the case. The behavior described above also applies to the ExtraBees inoculator.
To ensure that you're getting the most out of your serums, just imprint the princess and drone separately, then let your automation take care of them from there.