Some ships like Star Destroyers are bristling with weapons. Let's say a Star Destroyer and a Corillian Corvette are duking it out. Would you need to roll for every weapon in a firing arc separately? That might take a long time.

Do minion groups!

Determine how many minion groups you'd like to have acting in the encounter, assign each bank of weapons to a minion group, and then fill up the initiative slots as appropriate during the encounter.

There's different ways to do it. AoR has a thing where you can have every type of a single weapon in a single arc do a check to deal damage or create a sort of protective barrage around the arc. If it's more than just two big ships, there's Mass Combat rules in Onslaught at Arda I (which can still pretty much apply even if it is just two ships). Pg. 40-42 of the Operation Shadowpoint AoR Beginner Game Continuation Adventure also has some tips on different ways of handling big battles full of NPCs, including a more simplified version of Mass Combat rules.

And you could just assign a handful of NPCs in charge of whatever feels right and stick them into normal initiative slots.

Edit: LINKS

I recommend giving the capital ship episode of the Order 66 podcast a listen. They discuss all this in detail