I could only find contradictory information on this matter. Pretty much every MoO2 site out there seems to have its own school of thought...
But if you have the time, you should be able to test it yourself. Start an easy game, expand as much as you can, and avoid researching any targeting computers technology until you have some good armor or shields. Meanwhile build some carriers, preferably Battleships with reinforced hull, and start researching Cybertronic Computers. A few turns before completing the project save the game and send your carriers against targets with good (100 or above) Beam Defense. Alkari ships should be a good targeting pratice, since they have a +50def racial bonus.
- See if your fighters have troubles to score a hit, if necessary reload and repeat the fight a few times to be sure.
- Reload and repeat the fight once you have researched Cybertronics, but don't equip your ships with it.
- Repeat again once you've equipped the computers in your ships.
Regardless of the result, I'd like to mention that even if you don't plan to use beam weapons offensively, ignoring targeting upgrades might not be the best idea, since you're gonna need them for your PD weapons anyway.