The reason is that prior to 2006 the silencer (all of the silencer) was in the very large tube on the right side of the bike. A long exhaust system allows the factory and aftermarkets to tune the power and torque to different areas of the RPM range. In 06 they started incorporating all of the exhaust system including a catalytic converter into a box under the bike. It still has the length but it makes the exhaust to flow back and forth a few times before exiting out the side of the bike. Longer exhaust + catalytic converter = less noise needing a smaller silencer.
You can shorten the silencer if you want but it will affect the noise level and make the bike louder. If you make it too short it may have an effect on power but I imagine you would have to make it really short as well as shorten the piece of pipe in front of the canister to affect performance enough to feel a difference.
I just shortened the V&H on my YZF750R but only because for cosmetic reasons, the pipe had a bit of road rash that I wanted to get rid of.