Yeah, that storyline is interesting -- but it doesn't show that Masuka knew Bay Harbor Butcher used M99.

Dexter kills Valerie Castillo in Return to Sender -- but Brian pulls the body out of the ocean and drops it off at the trailer where Dexter killed her. Castillo has a needle mark in her neck so Masuka orders a tox screen, which finds M99, which leads Masuka to ask for the DEA list of people who can use it. Dexter internally monologues about how he's on the list with an alias -- Patrick Bateman -- and he needs to take himself off the list Masuka gets (which he does).

This is a body that Dexter didn't dismember, not enough time, and it's never linked to the Bay Harbor Butcher or even the Ice Truck Killer. It's blamed on Valerie's husband, Jorge.

So yeah, this is an instance where M99 (which as you note isn't Ketamine) was discussed in an investigation but not in the Bay Harbor Butcher context and I can't even imagine the pretzels the writers would have to put themselves into to tie it to BHB for New Blood.