Yes, strongly amenable subfactors of the hyperfinite $II_1$-factor are completely classified by their standard invariant. The finite depth case was done by Popa's Classification of subfactors: the reduction to commuting squares (MR1055708), and the infinite depth case was finished by Popa's Classification of amenable subfactors of type $II$ (MR1278111). The reconstruction theorem in this case reproduces a hyperfinite $II_1$-subfactor.
The Guionnet-Jones-Shlyakhtenko construction reproduces an inclusion of interpolated free-group factors (arXiv:0911.4728), and there is a specific formula for which factors you get. So you need to start with the right factors (modulo the free-group factor isomorphism problem...).
Noah's answer makes a really important point. I should point out that at index 6, Bisch, Nicoara, and Popa constructed an uncountable family of (non-amenable) subfactors of the hyperfinite $II_1$-factor with the same standard invariant with property (T) (MR2314611). As they say in the abstract:
We exploit the fact that property (T) groups have uncountably many non-cocycle conjugate cocycle actions on the hyperfinite $II_1$ factor.
For a discrete group, if you're amenable and you have property (T), then you're finite. For a subfactor, if you're amenable and you have property (T), then you're finite depth. So once you're in the infinite depth property (T) setting, there's no hope for a bijective correspondence between subfactors and planar algebras.