I think this is a reasonable enhancement request that could be mostly implemented with not too much work. The three areas as I see it are:
* GTK theme: You can request to be put in "dark mode" like in [@b4n's plugin](https://github.com/b4n/geany-plugin-dark-theme/blob/25fa14a97c2c1f1b1a2d7da3...) which is just a few lines of code.
* Scintilla theme: Not counting actual dark themes, this could be done simply using the existing "invert syntax highlighting colors" functionality.
* VTE theme: I guess this would be similarly invert the foreground and background colours using the libvte API.
Due to above, re-opening and labeling as an enhancement.