When the flight has a stop at HAA, it's technially 2 flights, and therefore you won't earn any qualification segments or EB points in this case.
For the direct TOS-HFT flight. Please look careful at the flight plan when you book. Sometimes the airlines sells the flight as direct, but when you look at the details of the flight plan, there is a stop and the 2 legs might have the same flight number. If this is the case for the direct TOS-HFT flight and the stop is at HAA, you won't earn qualification segments or EB points on the direct flight either.