Great, that you have it reported on Debian. And good to know that newer versions of the theme do not expose this bug. Debian users could probably even install the Sid package (judged from the direct dependencies which should be possible).
Back to Geany: I fully agree with what @techee said. It's not unnecessary work as we have to do anyway in the future (if we don't find a way to burn GTK4 before...) and it prevents users from having a bad first impression of Geany and/or the update to the new version.
Might there be any risk that other themes may not work well with the changed icon references? I guess this is hard to answer; the icon loading mechanism are big mystique to me and so I'm just wondering how much we could break with this change.