fmincon does not know or care about the internals of your objective function code. You can do anything there, and call whatever subfunctions you wish, as long as the input/output relationship of the overall routine is that of a twice continuously differentiable function. The same with any nonlinear constraint functions you might supply.
In case it matters, though, note that fmincon will treat your unknown n(i) variables as continuous variables. You have no way of constraining the optimized n(i) to be integers, for example.
