When you say 'always' do you actually mean 'always' and with all aircraft?
I only ask because I've seen plenty of occasions where that's not the case.
The answer is "Yes". ALL aircraft that trap (so obviously rotorcraft and VSTOL aircraft are exempted) aim for the 3-wire. The meatball (optical landing system) results in the same glidepath for EVERY aircraft and that glidepath takes them to the 3-wire. If the glidepath were different for different aircraft, both the meatball and the LSO's eyes would have to be recalibrated for every aircraft. It's difficult enough to keep up with changing the arresting gear engine's calibration for different trap weights. (When they roll final, the pilot of every aircraft calls the ball and states their type of aircraft and fuel state so the arrestor engine can be properly set.) It would be nightmarish to have to recalibrate the meatball and the LSO for every different aircraft. If you land long (or the carrier deck drops down during heavy weather) you have one extra wire. If you miss that one, you go around and try again. Landing short risks a ramp strike (hitting the edge of the deck) which is generally fatal, so the 3-wire is much preferred over the 2-wire.
BTW, I heard but cannot confirm that CVN-77 and later will have only 3 cross deck pendants (arrestor wires). Can anyone confirm?