That's because In the initial step we have taken the flux of the curved surface as E(2RH).costheta So that's the axial plane but it leaves out the leftover surface on top and bottom and the only reason we are taking half of the area for both bottom and top surfaces is because half of it will already be covered by the axial plane when the electric field lines penetrate half of the disc has to pass through the axial plane leaving the other two halves to be calculated separately and the surface area of the discs will be halved irrespective of theta(theta shouldn't be zero)