He didn't say that he did.
He said, ""[P]erhaps, at some future date, this Court will have the opportunity to determine whether Justice Story was correct."
He suggested the RKBA is a personal right. Then he cited Justice Story on the RKBA by citizens. Why would he cite Justice Story in the context of his remarks if he didn't agree?
Just exercising his rhetorical skills?
He cited Justice Story to support the conjecture.
I can make similar statements regarding UFO's, talking about a growing body of scientific commentary, and early hisorical writings, and even a quote from Art Bell. Does that mean I believe in UFO's?
That said, Justice Thomas may indeed consider the RKBA the key liberty of a republic -- it's just that he didn't say it, that's all.