Yes, Scintilla can use the cursors [here](https://github.com/geany/geany/blob/3a92129d61d4d8e96136e29d4709bb638527be40...) and it just asks GDK for them.
It is [documented](https://www.scintilla.org/ScintillaDoc.html#SCI_SETMARGINCURSORN) that a right cursor is shown over margins and Geany does not set it, just leaves it as default. A PR making a setting to select a different cursor would probably be accepted so long as default was as is.
Elsewhere Scintilla notes use of another cursor icon for clickable links, not used by Geany, but I think plugin(s) might use it.
A quick look at the discussion the OP linked seems to suggest that the problem is being fixed by linking under the old names as well as the new names, so I doubt its worth it doing anything in Scintilla or Geany. The problem should only affect bleeding edge rolling distros for a short time, and if it doesn't get in a release should not appear in stable distros.