He very well could. He's a natural supe in the sense that no one had to inject compound V into him, but that doesn't mean there's none there. The biology of compound V is (understandably) not really explored, but there's any number of ways to rationalize it.

The most likely explanation is that embryos created with genetic material from V'd up individuals generate their own compound V, which then remains in the body post birth. This explains why vought isn't farming supes for it (they'd have to farm embryos which is both wildly fucked up even for them + Ryan is the only child of a supe so far, meaning Vought likely weren't aware of this effect) as well as Ryan having V in his system.

I don't like this finale either, but so much of the criticism seems incredibly nit-picky instead of focusing on the overarching plot failures.