does the added strength of your military from resources actually give you a higher score? I guess the same could be asked of research and economic resources.
Definitely yes for econ and research, yes also for militrary resources but only if you have noticeable numbers ships to apply the bonus to.
Basically you get credit for your "military ranking" that's listed under the Stats & Graphs tab of your civilization manager. This is listed in the Military section under Abilities. This is not to be confused with military might shown in the bar graph which is actually the ratio of your military ranking compared to that of the currently selected AI.
Anyway since your military bonus multiplies the attack and defense value of your ships then military resources increase your score as long as you have large numbers of ships. If you don't have any ships then military resources do nothing for your score.
I looked at a few other ships and all of them had increased attacks after launch but defence values stayed the same.
I've never seen or heard of anything like this, in fact this is opposite to what I would expect to happen. Your military resource mining bonus applies equally to ships in flight or in orbit about a planet. However you actually get a 25% bonus to attack and defense values (rounded down) while a ship is in orbit, so a ship with an attack value of 42 (regardless of what bonus you have) should have an attack value of 52 if parked in orbit.
So what you describe really doesn't make sense. The only thing that I can think of is if you have any military starbases (as opposed to military resource mining starbases). In this case as your ships come into the military starbases area of influence then their attack values could increase.