I doubt that the shield gets ignored by the second hit if the other character is on your side. I'm pretty sure that when someone wanted to block both hits (and knew there would be a second hit coming from my Usmash), they could do so just by keeping the shield up.
But this might depend on a couple things though. I know that in Melee you could direct your shield up, down, towards the front using the control stick. I haven't noticed that in Brawl (you probably can, I just haven't really checked to be honest lol). So, what I'm driving at is, MAYBE, the second hit of the Usmash somehow hits under or over where your opponent happened to direct his shield at that time (whether he knew he was directing his shield or not). But all this depends on if you actually can direct your shield.
Either that or, like I said, he dropped his shield to counter, not expecting the second hit and got smacked by it. I don't recall ever hitting an enemy next to me with just the second hit, but if it does send them flying horizontally, it would really be a rather unpredictable trajectory to try and DI.