I think it's mainly a tooling issue—readme files are repo "homepages" by default, there isn't an easy way to inline an image in Markdown (nor should you want to), and people don't want to pollute a repo with binaries.
There is something about the github itself, or the culture around it is the issue, since the problem seems so pervasive. I would prefer the site fosters better project information.
Compare github project pages to what you would find at the now defunct codeplex. The difference was night and day.
I still don't follow you; why is this an issue with markdown? Why do you see this as different than any other markup language (e.g, HTML)? Unless we're talking about something like Word documents, you'll have to host the image somewhere, which could be in your github repo. I still don't see why this is an issue.