If your dealing with fighters from outposts(ninja jetbikes) they have extreme dodge bonus of +50, on top of being a very small target. Dodge cancels out your accuracy bonus and then starts eating away at base to hit chance, which in the case of small target is already reduced.
I don't know what your pilot bonus to accuracy is, but the final to hit chance is probably near 0, and may even be zero.
Until you have really good pilots your better off doing bait tactics.
The fighters spawned by enemy bases have a cooldown after the return to base. Launch something besides your misson craft, get the fighters to pop and immediately return to base. Wait for fighters to return home then send out your actual mission craft.
Alternatively hunting parties are immune to intercept.