In episode 6, “All-New Halloween Spooktacular!”, Darcy is shown rifling through the digital secrets of S.W.O.R.D. and in the process a brief glimpse is seen of a medical file labeled “Johnson, Ray.” While this is admittedly not the most distinctive of names, it happens to be one of the multiple aliases by which John Wraith has been known. Of course, the character’s appeared on screen once before in X-Men Origins: Wolverine where he was played by will.i.am, but that’s unlikely to be referenced as everyone involved in that notorious misfire probably wants to forget about it.
Although Wraith is a mutant with the power of teleportation, it’s an ability he uses only sparingly and never within sight of others if he can avoid it, preferring to rely on his skill with weapons, particularly explosives. More relevantly, he was part of the Weapon X program alongside the likes of Wolverine and Sabretooth, so it’s not much of a leap to guess that the black-ops genetic engineering project already exists as a clandestine division of S.W.O.R.D.
Of course, the presence of mutants has been much less obliquely suggested by the “recasting” of Quicksilver to Evan Peters’ iteration of the character from Fox’s X-Men movies, although his provenance and authenticity is still somewhat in question and yet to be fully clarified.
With Marvel’s extensive history and litany of characters, it’s no problem at all to pluck out a random name as an Easter egg, and while Ray Johnson isn’t as definitive an identity to tie to Weapon X as, say, James Howlett or Wade Wilson would be, WandaVision pointedly showing it still demonstrates that plans to bring in mutants can’t be far behind.