[zenith]

During wars the weapon that causes the most damage to a hideout is used.

In PvP battles, the weapon that causes the most potential damage is selected (best weapon). This however doesn't mean it will pick the weapon that YOU cause the most damage with. If you have an ionized axe and a t-250 shotgun equipped and you have specialized in ranged combat, it will pick the axe because it's the best weapon. Even if you cause more damage with the shotgun.

So in summary, in wars you can't go wrong equipping 2 weapons. In pvp fights though you might have the wrong weapon being selected, although it is pretty rare.