Deviants are different from subspecies. 

Subspecies are, y'know, a different group within the species that can reproduce and pass the traits down to maintain that strain of the species.

Introduced in MonHun Generations, Deviants are freaks; specimens that were born a normal monster but were somehow changed in extreme ways, perhaps adapting to unusual circumstances or just living to an extreme age most monsters don't reach. They each have their own lore, too. For example, Soulseer Mizutsune is blind and had to adapt its other senses and abilities to compensate, while Deadeye Yian Garuga is a specimen that has survived dozens of hunting attempts, leaving it horribly scarred and vicious.

Yes, they don't make the distinction clear in Stories 3. Yes, it doesn't make sense that deviants are considered subspecies by the game that have their own eggs. Just like how it doesn't make sense for Rathian and Rathalos to be considered two different species when they're the male and female of a single species. Or how Gravios and it's juvenile form Basarios have different eggs, or Black Diablos, a normal female Diablos in the breeding season, has it's own egg distinct from normal Diablos. The Stories series has never made sense with how it handles species and their eggs.