OP
1. How about just make strat targets only worth a certain fraction of a real base structure like a hangar? For example... town building = 1/4 a hangar, city house = 1/10 a hangar, etc. So when you drop a stuka nuke on a city and blow up 20 houses your hit % is really only 2%, not 20% or whatever.
2. Not sure this is within the confines of the scoring format. How would this adjust for hit %? I feel like everyone generally gets an even look at bombers each tour and there definitely is a risk factor going after them. Imo, only a big deal if someone is shade vulching them.
3. Similar idea, more efficient, more complicated.

Minimum Missions Flown Formula would be as follows:
You take your total individual ranks added up and divide it by variable Fm (Min Mission Factor) Fm will level off as your mission # goes up.Fm will be a number that approaches 1 as your missions increase. For example if you have only 10 missions flown, your Fm # will be like 0.5, If you have 30 missions flown your Fm # will be like 0.8 if you have 300 missions flown, your Fm will be 0.9987 or something.
The Fm curve would have to be opinionated at what HTC would deem "reasonable number of missions for a tour" For example, 1 Mission a day would get you 30 missions, which would probably be good enough for like a 0.8 Fm or something. This would be a good way to still give rank to players with only a few missions flown but penalize them as far as overall ranks go for not flying a reasonable amount to be considered for top ranks.