Yeah I did mine a while back, kept to straight lines and it looked awesome. Then I took some steel wool (fine) and did it again, because the steel wool is so fine there are no lines visible, it sort of polishes it out. I love the look...even scotched the shock caps and my chrome turn signal stems.
Yes, it will absolutely rust. How soon depends on how much chrome you remove, but it will eventually rust irregardless. Good clear coat paint will help prevent the rusting, as will diligent maintenance (i.e., clean it often, and steel wool rust spots off as soon as they appear).
Yeah I figure, I'll keep scotching them clean till I get new pipes next year or so. I'm wondering if I'd find any kind of clear coat that can stand the heat. Anyway...removing the heat shields and wrapping the headers so its only the mufflers to think about...LOL, I could always remove the mufflers ^_^