If you enemy is firing catapult missiles, and you put a buffer of fighters between you and his incoming missiles will they take out the incoming catapult missiles?
Full physics simulation. If a shell or missile hits something, it damages it, regardless of whether it is flying or not. Fighters don't shoot down missiles (at least there isn't a plane with point defense yet; there might be), but if a projectile hits an aircraft, it stops it. (Gunship type aircraft that have some point defense capability against missiles might actually be interesting, as it would make gun-type AA more effective than long range missiles at destroying them.) But, yes, you can physically block a projectile with aircraft. But ideally the cost, build time, and HP of ground units and air units should be such that you do not want to do this. The plane should be much more valuable to you than almost anything that the incoming missile or shell might hit on the ground.
Yes it can, I recorded it happening and posted it in the forums since it seemed cool. Like ledarsi said though, it isn't even remotely cost effective.
Point defense is definitely a cool thing. Unfortunately, no unit actively intercepts missiles at this time.