[PvK]

I think it depends somewhat on the exact match-ups. To-hit chances are important. For example, if your ships are hard for the enemy to hit, then being able to survive a few hits (or even just one) and still fight as well, can multiply a ship's effectiveness. On the other hand, if your ships are going to get pounded regularly, then it might make sense to try to get in as many shots as possible before they die.

Also consider cost. Weapons are more expensive than armor, especially organic armor, so the side with armor may be able to build and maintain more ships. Emissive armor looks better than regular armor until you consider the cost - it only seems to work well if you have a lot of tonnage to dedicate to it, and get one or two and then combine with lots of regular armor (not organic). Even then it's not that great, especially against powerful mounted weapons.

I can think of several other considerations which apply in different circumstances, too.

PvK