EMP and Hacking behave differently and affect different units
In the original Generals, EMP and hacking seemed to be largely the same in that they both tended to have the same effect on the same units. The main different was that, with the exception(?) of the Microwave tank, EMP was an area of effect weapon while Hacking affected a single unit/structure. Also, consider the Generals-inspired C&C3 mod MidEast Crisis 2, where hacking/computer viruses are generally treated as friendly-fire-proof EMP and nothing else.
The idea here is to distinguish the two weapons mainly by having them affect different units. Specifically, low-tech units tend to be vulnerable to EMP but not hacking/viruses, while high-tech units tend to be vulnerable to hacking/viruses but not EMP. (If you need a justification for this, consider that most modern cars run off a computer that would be vulnerable to EMP but that probably isn't connected to any sort of network; conversely, high tech units might either have better EMP shielding or run off of computers that aren't vulnerable to EMP, such as a biocompter.)
In that light, EMP would be a high-tech, area-of-effect weapon that helps the high-tech units compensate for being significantly outnumbered by low-tech units. Conversely, hacking/viruses would be a low-tech (maybe even tier 1) weapon that is targeted at a single unit and helps take the bite off your opponent teching up before you.
-More diverse mechanics/units
-Helps a low-tech player defeat a higher-tech player/helps a high-tech player fight a player with a better economy
-Could lower the benefit of having good macro by allowing players to nullify your numerical or tech advantages
-Might make teching up less of a priority if your opponent can freeze your Mammoth Tanks but not your Predators.