Air game progression is fine, actually.
When still in airbus, stay away from any shipping that has a radar circle drawn around it.
When you contact the car thieves, megapol patrols start. It's tied to that research. Now you can get an aircar and an airspeeder. With the aircar you shouldn't try to intercept anything that shoots back, and missiles for the airspeeder are quite expensive. A seagull costs more than the loot you get from a megapol patrol car. But with the airspeeder, you can take a peek at most megapol craft, because it's fast enough to run away. And the megapol interceptor and chaser are quite rare, and it's quite obvious that they are faster than your average patrol car. Megapol craft tend to fly close to or at max speed, so spotting the faster craft is quite easy.
So with an aircar, you still stay away from shippings that have a radar circle, and any seagulls you might have in your airspeeder you will save for jucier, larger shippings.
Bandit flights start in june of the first year, but with them it's the same deal as with megapol.
So you can see, trying to shoot down even the weakest hunter killers will only become actually a good idea once you get better craft. So either codex craft, a shark jetbike, or a piranha airbike. For the jetbike, the rule is: if it's faster than you, it's too dangerous anyway (fighters for example). From everything that's slower you can disengage and run away, so you can take a look before deciding to fight. Airspeeder and piranha airbike can do that as well, to some extend. All you have to do is learn to watch a shipping a bit before you intercept, to get an idea what it's maximum speed is.
So the problem of not knowing what shippings to intercept mostly exists just for the medium fast codex craft. Here the safe option is to just go after megapol and bandits. These are easy to identify by their flight path, they travel from continent to continent like civillians. If you want to do more serious air combat, get a jetbike for recon and fire support. It's not that far away in the techtree.
Bottom line: for hunter killers, higher speed = more dangerous. Pretty simple rule of thumb.
Edit:
Ok, there is one air combat "trap" you can fall into that should be mentioned. The Bandit Mosquito has an avoid bonus of 35 and the Megapol Interceptor a bonus of 30. That's high enough that you might not be able to hit them with a 25mm x2 cannon or 30mm cannon, depending on your craft to hit bonus and pilot skill.
I'm a bit unsure on the math though. Accuracy formula for a target that has no avoid bonus is: (weapon accuracy + craft bonus + pilot bonus)*target size
(target size multiplier is 0.75 for very small and 0.875 for small)
Now the question is where the avoid bonus is subtracted. I would guess it's subtracted before multiplication by the size modifier.
So lets say you fly a Scarab with a 25mm x2 cannon (25% acc) and two quad cannons (15% acc). That is some serious firepower you would think. At 70 firing skill of the pilot, you get a +6 bonus and can *barely* hit a Megapol Interceptor. You will still loose most likely, because you only hit one shot in 100.
If you go with maxxed pilots of 122 firing skill, you get +26 bonus. Vs the Bandit Mosquito, that will still be a gamble of a fight (about 60% win chance).
So these are examples where you would think you have enough firepower, but actually don't. And you can't disengage because you are not fast enough.
The Ninja Seeker with its 40 avoid bonus is the worst, but at least you can easily identify them by their large radar circle.
