GTK3 Geany will not compile without deprecation warnings, but AFAIK GTK2 Geany will, so disabling deprecated interfaces should not affect a GTK2 compile if I understand `G_DISABLE_DEPRECATIONS` correctly. But since GTK3 Geany uses deprecated features anyway, I don't think the `--disable-deprecations` is tested any more, so it appears there are problems with it, either on the Geany or GTK side. It is more likely that the option will be removed rather than effort spent on fixing it until the GTK3 deprecations are removed (and its not clear how to do that and keep functionality in some cases).
Why were you setting that option? If you have no need to, then simply build Geany without the option (and probably `make clean` after changing it).