Since Git has the ability to keep track (and keep it clean) of branches with completely different content from each other, in the same repository, some projects (like Git it
I think it depends on what your project is.
Git is obviously a community OSS project so having the docs in the (same) repository so everyone gets them makes sense (to me).
On the other hand I would not store the docs for my projects at work as I would rarley edit them except on 'let's update the docs' type of ticket. At work I don't want my docs intermingled with my source, I just want the source (typical programmer view i know).
Others may want them all-together. I think you just need to realize what it means (remember everyone has a full copy of the repository) and pick the best option for your project.