I like to make a .local folder at the top of the project, which contains a .gitignore that ignores everything. Then I can effortlessly stash my development notes there without affecting the project .gitignore or messing around within the .git directory.
I agree with you. Empty .gitignore would be a "smell" to me. Whereas .gitkeep tells me exactly what purpose it serves. I like the semantic difference here that you describe. I don't like when multiple .gitignore files are littered throughout the codebase.