Hill function and stoichiometric matrix: confusion about reaction rates
If the reaction is $\ce{aA + bB = pP + qQ} $ then we define the rates as 

$$-\frac{1}{a}\frac{d[A]}{dt}=-\frac{1}{b}\frac{d[B]}{dt}=+\frac{1}{p}\frac{d[P]}{dt}=+\frac{1}{q}\frac{d[Q]}{dt}$$

As to the Hill function it seems that the complex nSX is just one species.