The rotors of a 8 years old bike with that mileage should be close to new.
If the pads have disintegrated due to some chemical exposure, you may be dragging the steel of the pads against the rotors, doing some damage.
You may have some internal rusting going on if the fluid is still original, since the fluid degrades in around two years and should be fully replaced.
Valves tend to make less noise when the service time is close.
I suspect the cam chain tensioner is dry and some lubrication may help.
I would service the brakes right away:
http://faq.ninja250.org/wiki/Brakes