It is extremely difficult to prove the weakness of the enemies through in-game methods. The standard response is "use the damage type of the faction who's space they normally appear in" (with amarr being as much thermic as EM, and rogue drones being vulnerable to EM, and kin/therm being interchangeable based on skills.) The common wisdom also says that the resists for NPCs all the way through shields and armor are the same, unlike players where the shield and armor weaknesses are different.
However, while trying to find you some concrete numbers from a data dump, I found this
. I'm not good enough with the math to figure out what the most effective damage type will be for each particular opponent, but my first glance seems to suggest that thermic might almost always be the best (which I can't say goes along with my in-game findings so much.)
Remember though, many missile ships will have bonuses to a specific damage type that might throw off what your guess might otherwise be.