After thinking about it, I would say yes.
First I thought no, because of the reasons you mentioned, but there are questions that regard the combination of apps and readers. Examples for this could be whether reading the same book on multiple devices (e.g. cell phone and tabled via an app and the ebook reader) is allowed by drm or how the reading process can be synchronized.
I also would like to see questions about the conversion of ebooks (e.g. with tools like calibre). So when questions about a tool that allows viewing and modifying ebooks should be allowed, why shouldn't be questions about a program that only allows viewing them?
Finally since the proposal is called "E-books and E-book Readers" (and not "E-book Readers") I think applications and devices that are designed for the main purpose of using / editing / managing ebooks should not be excluded.