Apart from what seasurfer pointed out, that "doko ni arimasu desu ka" should be "doko ni arimasu ka" without the "desu", those two sentences mean the same thing, and in every situation that I can think of at the moment, they are completely interchangeable. I think that you will hear "zasshi wa doko desu ka?" more than "zasshi wa doko ni arimasu ka?", simply because the second one is more of a mouthful and sounds more stilted.