Many reasons.
The biggest problem with the parking brake is that the damn thing never works, it has to be constantly adjusted as the brake pads wear out, and even adjusted properly it's not strong enough to really depend on it.
When it gets out of adjustment (takes about 8 hours of riding or less) it creates slack in the cable, which releases pressure on the parking brake safety switch which is on the clutch perch. This sets a 2,000 rpm rev limiter intended to keep people from riding it with the parking brake set. This makes people go nuts trying to find what the problem is, people think it could be a carb problem, bad cdi, bad coil, bad stator, the last thing they think about is a parking brake sensor.
The stock clutch perch sucks, the pivot doesn't have any bushings or bearings, so it wears out quickly and has a hard, rough pull compared to a simple $30 aftermarket one. The old design adjuster is also a pain, with the new ones you can adjust it on the fly, no need to even slow down. Removing the perch also clears up some space on the handlebars and looks better.
The parking brake assembly on the caliper also causes difficulties when installing new brake pads. If it's not fully adjusted out it'll keep the caliper from sliding all the way back in, thus creating numerous other frustrations. It's also a place to potentially leak dust, water, and other contaminants into the caliper, seizing the piston and ruining it.
So in summary, just makes things easier in the long run, and the thing doesn't work right anyways.
