I agree with darrsi, my yamaha stealer said the stock pipes are much better than aftermarket ones, they are basically made better by a manufactorer, although in mild steel, which ain't great.
If they are in reasonable condition take them off clean all the rust off and then respray with high temp paint, that will help protect them. Also saves you about 150 quid.
If you leave it too long you will get rust holes on the collector box, trust me i know, i found this out 3 days ago.
I'm taking mine off, welding them up and respraying.