If you're concerned about the accuracy of the Bestiary, then why not suggest that killing Hardmode equivalents adds Bestiary and banner progression while not adding to the displayed kill count? For instance, killing 50 Moss Hornets gives the complete entries for all Hornet variants and gives the Hornet Banner even if you haven't even seen a Hornet before, and the Bestiary still claims you haven't slain a single one?
The game already does part of this for the Salamander, Giant Shelly, and Crawdad trio; since only 2 of those 3 spawn per world, completing the 2 entries you can complete also completes the 3rd entry you can't complete.