Holes in the expansion chamber..

The holes were probably plugged from testing, I know Honda has done this for pipe temp testing, etc,,,,,

Maybe it was like we did when we were kids. Remember putting playing cards in the spokes?

Honestly, what if they found weak spots in their pipes? The holes may have been used to stop drill the cracks from getting bigger.

I still like the "testing" idea better.

Those holes are water-mud drains for his pipe guard. At least that was my first thought, but after seeing the pics from High point and the location of the holes in the front of the guard. It's my guess it's too help keep the pipe temp down while using the guards for protection. As the tuning of a pipe in part relies on it's temp. Those guards without holes could insulate well enough to change the tuned length of the pipe. That would then shift the powerband up towards the top end and take the motor out of the optimum spec, they found when testing without the pipe guards. 

Would these be the holes your talking about? Steve is right they're just air openings to keep the exhaust temp. within spec.