I'm pretty sure you can't access the files you downloaded from newsstand.com without the proprietary reader. And the DRM prevents you from copying too.
I had a very bad experience with the DRM of newsstand.com after upgrading my PC. I suspended the account just before the end of my subscription and for some mysterious reason, they refunded whole amount. I can't really complain about their service since I got all my money back but I think their DRM is unnecessarily tough.