Powerful enemies are hard to destroy via damage. Check their immunities and anything NOT listed there is their weakness that will work better than dealing damage. Additionally corruption resistance <75% should be treated as a weakness. In case of combat programmers you can use a core stripper, disrupt & rewire, melt them and a few others. They always use EM weapons, so get some EM resistance.
Q series have somewhat randomised components, but shorter list of immunities, so there are even more ways to deal with them (and they have even more health, so damage is even worse against them).
A lot of items found in Q or T make short work of intercept squads.
Keep eyes open for explosive machinery -- they can deal TH, EM or EX damage, so only the first one is useful against combat programmers.
As for flight builds (and maybe hover too?): I hear that people just fly away.