I don't think multiple stores will be all that big a problem. Publishers will still want to provide their books via Amazon and other one-stop shops too due to already established customer bases. Having their own store will just give them wiggle room when it comes to future negotiations, especially if they can grow their own direct sales base sufficiently.
As for multiple logins, yes it's a pain the first time you setup at each store, I already shop at Amazon, Baen and more recently Kobobooks. Once you're setup though it's not all that much of a problem. In fact, multiple logins isn't an issue, it's more having to setup everything that the DRM required that bugged me the most.
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