The splitting of invariant manifolds of whiskered (hyperbolic) tori with two frequencies in a nearly integrable Hamiltonian system, whose hyperbolic part is given by a pendulum, is studied. We consider a torus with a fast frequency vector $\omega/\sqrt\varepsilon$, with $\omega=(1,\Omega),$ where the frequency ratio $\Omega$ is a quadratic irrational number. Applying the Poincare--Melnikov method, we carry out a careful study of the dominant harmonics of the Melnikov potential. This allows us to provide an asymptotic estimate for the maximal splitting distance and show the existence of transverse homoclinic orbits to the whiskered tori with an asymptotic estimate for the transversality of the splitting. Both estimates are exponentially small in $\varepsilon$, with the functions in the exponents being periodic with respect to $\ln\varepsilon$, and can be explicitly constructed from the continued fraction of $\Omega$. In this way, we emphasize the strong dependence of our results on the arithmetic propertie...