Scintilla creating so many new windows on X11 causes problems. There are bugs like this one that cause XServer collisions that have been observed with Geany/Scintilla and with GTK3 sometimes it causes windows to be lost.
Depending on the computer/system sometimes this can cause severe performance impacts also. For example, on my computer with Geany built for GTK3, after a lot of use (with lots of "tags" that cause many autocompletion windows), it can cause window creation such as opening dialogs to take many seconds. I believe it's a bug/problem in XServer or GDK that is only exposed more regularly because Scintilla is creating so many Windows.
Colomban Wendling has made changes to Scintilla platform to cache the autocomplete window for GTK+ platform which I have been using for a couple of weeks and it seems to solve the XID collision problems (not experienced by me) and the massive slowdowns on new window creation that I was experiencing. I will contact Colomban to see about posting the patch for review and/or adding additional information.
Disclaimer: I'm making the assumption that too many new X windows is causing the problem, but it's completely unproven, all I can be sure is that with Colomban's cached window patch, my performance issues go away. I'm fairly certain it's a GTK/GDK/X11 bug that can be worked around fairly simple.