I have a masters in computer science here in the USA, and I hate it. The government won't send me welfare checks because I'm too successful or something. I didn't even get in on that stimulus we had last summer because I made "too much." How lame is that? I'm going back to flipping burgers.
All jokes aside, I think it gives me a leg up on people with a BS degree. I worked as a software engineer while I went to school, and I find that most job listings want x to y years of experience with a BSCS or (x-2) to (y-2) years of experience with an MSCS. Since it only took me a year to go through the masters program (double time, while working!) I think it paid off.
Ultimately, however, it depends on what you want to do as a career. Do you have your bachelors yet? It should be easy to double major in CS and chemistry if chemistry is what you love. That gives you time to think about which one you'd like to specialize in. Of course, you could always get two MS degrees. 🙂
Why not just combine the two and work towards a career in bioinformatics? You'd need some biology, too, but then you can use your computer skills to help develop cures for things.