It was a lot easier than expected to change hyblog to a date-based folder structure for posts and comments.
To get all post and comment files, to build the next/previous links, I was using:
glob($target_dir.'*.md')
Moving to a yyyy/dd date structure meant that I just needed to change this to:
glob($target_dir.'*/*/*.md')
Because the view is organised by a date check I then just needed to change the file paths to save/update the files. Everything else takes care of itself.
This could get quite heavy if there were years worth of posts but it could be done in the background with a cron job. At the moment, with only a few days, it's still very quick.
Three of four goals set for this weekend achieved already!