[X] 0: Ten Saucer Type-1 Phasers (Infra++) [Avg Damage: 9]
[X] 1: Two Forward Photon Launchers (Infra++) [Avg Damage: 1.5] [Alpha Strike: 36]
[X] 2: No Aft Torpedoes
[X] 3: Two Engineering Section Type-1 Phasers (Infra+) [Avg Damage: 2]
Here's my reasoning: start with the forward photon launchers, because they're the most straightforward decision for me. We've been wanting to prototype photon launchers, and the Copernicus needs better alpha-strike and single-target damage. Two forward photon launchers check both those boxes nicely.
Then the phasers. Six phasers aren't going to cut it for a ship this size, so we need more. I don't think eight is enough, either, which means I have to go for at least four phasers on engineering or ten on the saucer. The saucer ones offer more damage and have better firing arcs, so ten saucer phasers it is.
So then it's just the engineering section left. I do the phasers first, because I think there's a clear winner here: Ten phasers is nothing to sneeze at, so zero phasers is workable but I still think the ship needs a little more oomph. Four engineering phasers strike me as excessive: as tempting as it is to go full dakka, this ship also needs resources to do SCIENCE!! with and a double Infrastructure cost is pretty steep. Two engineering phasers offers some very efficient damage, at 1 damage per phaser for only a single infrastructure cost. I also don't think we've mounted phasers on the engineering section before, so that'll be nice.
Finally, we get to the aft torpedo options. The extra alpha strike damage is nice, but the sustained damage they offer is mediocre. They do only cost one infrastructure, but even that cost is tough to justify on an already-expensive ship. I don't think we need any of them, and we already have two forward launchers. No aft torpedoes it is.