Should I put the raw data in the appendix of an investigation if it is available in the GitHub repository?
There is no need to put the data into the paper itself if it is accessible and you point to its location. For a printed paper it is mostly useless, of course, and if it is online, then it is only a click or two away. No one is likely to complain about the minimal added effort.
But, like any other web resources, your reference to it should include a date (last referenced). Then if it is later changed for any reason, the reader will have a better sense of what is going on.