It’s not confirmed, but there are rumors that HTC may come out with their own app store which will have both e-books and apps, and it might be a part of their HTCSense.com website.
HTCSense.com is already available for Android handsets, especially the HTC Hub section which lets you browse for apps and 'like' them.
There’s also a story that HTC is not happy to just customize the UI for Android but would also want an app store with it. It seems that they are hiring a team for this, and hopefully should integrate well with HTCSense.com
HTC has already partnered with Kobo to pre-install their readers on the phones, but there are chances of e-books being offered by the HTC store while the books will be provided to them by Kobo.
Microsoft has never had a problem with manufacture-branded sections in the Marketplace and yes HTC can cater to it’s Windows Phones users as well. Let’s hope for the best.