It knows where to hit because it uses 1990s AI... and thus it cheats a little. ; )

But you can do the same thing. Once you get long-range radar, choose your long-range weapons and start Shift-clicking enemy dots (stick to the stationary ones) and let your big guns do their damage. Keep in mind that those long guns take forever to turn so you want to add targets in a single sweeping arc and not just by picking willy-nilly all over the place.

You might try building radar jammer units but I'm not certain that will help against the AI's long guns.

Really, your radar picture and long-range units can mess up the enemy pretty heavily without you actually knowing what it is you're shooting at. And every once in a while you'll get that lucky shot that takes out the Commander, fairly easy to do since he stays stationary while building.

And thus, that might lead to your solution: take out the enemy long-range radar to blind him.

Alternatively, or at the same time, build a few stealth fighters and send them zipping all over the place to reveal as much of his stuff as you can. Hot-key both your fighters and a long-range gun, so as your fighters expose an important target (including the Commander) you can hot-key your gun and set a target right away (shift-click for multiple targets), and then switch back to control of your fighters. I would prioritize radar, his long guns, Commander (for obvious reasons), and his anti-air missile launchers (to give your fighters better survival odds).

The nice thing about your big guns is that when they miss the target, odds are they're hitting SOMEthing. And they have a big boom radius.

That said, dunno if you need to rush for the super-cannons. For all the time and resources it takes, you can get a couple airfields cranking out Level 2 planes like crazy. Even the bombers are worth it but try to get the air defense knocked back a bit before you send them in.