That part about EM being roughly as effective as other damage types against CProgs is outdated. Now EM kills CProgs ~4 times slower than the other damage types.
Let me post an updated tip:
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.
A bit more specifics about fighting CProgs: Get some EM Shields or better. Dynamic Insulation Systems help too. You can get 90% EM resistance from Damper Plating, available from Wastes. Molecular Deconstructor works splendidly, if you are lucky and find it in caves. Most weapons (except for EM and EX) work well enough (melee works too!). I used to melt them with plasma weapons (in case of bad rolls when you miss their core too often, they'll just melt) or disrupt and rewire them. You may also want to minimize time spent on each floor, so that you don't have to deal with multiple dispatches.
As for flight builds (and maybe hover too?): I hear that people just fly away.
