That depends on the environment of the server you're on... Are people there focusing on shielding and perhaps have a layer or two of armor at most, or are there players/faction that are packing armor out the wazoo? If there's lots of armor tanking going on you will want fewer harder hitting projectiles with some minimum block swarmers/rapids on a turret or logic clock to distract point defenses. If there's not much armor you can get away with having multiple computers and firing off weaker projectiles in salvos; they won't need to deal much alpha to get past a single layer or two and have the damage left over to take out the systems in it's radius.
Keep in mind that having more than one output on a single computer increases the energy consumption of the weapon as well as the block clearing capacity.
For anti-shield weaponry I will always prefer single outputs. Yes, there are exceptions such as logic operated weaponry or missile redundancy, but for all other cases the increased energy cost of having more than one output on a computer is wasted on shield.
For capital ship weaponry I base my weapons around certain points of damage/DPS, such as dealing enough damage in one shot to break a single advanced armor with pierce passive (4,000 EHP) with just enough left over to destroy a line of systems (5 HP each, so usually 50-100 damage) behind it and put a dent in the opponent's capabilities. If your cannon/beam is penetrating more than, say, 30 blocks per tick of damage then you need another output.
I tend to go for about 500 blocks per output on non-rapid block clearing weapons, and closer to 1,000-5,000 for the rapid ones since that's close to one of the cutoffs for damage to penetration ratio (Smaller cannons/beams have better scaling for penetration per point of damage output).
For smaller ships or weapons this doesn't matter as much, so the main points of awareness become reliability (how often is my damage potential being reached?) and effectiveness (should I have one cannon/cannon/punch or split it into a cannon/beam/ion and a missile/beam/pierce?).