Yes, we have several customers who publish subscription content in the App Store. They have all contacted us to enhance the original App we developed for them to support Newsstand, after they were contacted by Apple with regards to this new iOS 5 feature. Apple has given them deadlines to comply with the new requirement for subscriptions to support Newsstand.
It does not in any way change the fact that putting Newsstand into a folder is only done through the exploitation of a bug, and the practice creates a directory structure that is not supported by iOS.
My recommendation to not do this under risk of unexpected consequences would be the same whether or not we had any Apps that support Newsstand.
If you have subscriptions that use Newsstand, you cannot hide it anyway...