That's likely why it was changed. I keep deleting my extra 2 because "497 pets, 495 unique" is annoying. I welcome this change a ton.
Well, I guess on the plus side it'll stop that nasty issue where the multiple bigglesworths being forced into the pet journal was erasing some people's level 25s.
I assume it was changed simply because him not being unique was a bug. The behaviour was obviously buggy, and every other achievement pet was unique all ready anyway. Glad I can finally get rid of them and know they won't pop back up.
Edit; Simca, the new fish. Are they caught in any water in their respective zones, or do special fishing pools spawn that have them?
I assume they're open water catches. Something to work on while you work on Nat Pagle rep!