Does the "Impact" weapon proficiency increase all damage?

Short answer

It increases damage indirectly.

Longer answer

This has been a common occurrence since Modern Warfare I. The 'impact' weapon perk is similar to the 'deep impact' in the first one. While it doesn't actually increase the damage directly, there are a couple important scenarios to note here that could cause your weapon to do more damage.

The first:

Chances are you're shooting through surfaces more then you realize and the increased penetration is actually making your gun stronger. Most Call of Duty fights take place around some sort of cover (unless they are a total noob and roam the middle of the street avoiding potential cover) and while you're carefully aiming at their head or chest chances are you're going to miss and utilize your bullet penetration.

The Second:

Aah, the multi-kill. My favorite reason to throw on 'impact'. In Call of Duty, players are considered a 'surface', meaning that if two players were standing in a line and you shot the first one, the penetrating bullets would hit the second player for less damage then the first. Putting on 'Impact' can be the difference between clearing a room of four players and only killing the first.