Weird.
I saw in that debug output is the config directory `~/.config/geany` so just tried deleting that to start with default options. Still no horizontal scrollbar.
Also saw in `~/.config/geany` the actual config file and in there is option `show_editor_scrollbars=true` so tried changing that to `false` and it did get rid of the vertical scrollbar. But when I turned it back to `true` just the vertical scrollbar comes back.