I am using the latest version of citra in the releases section of this github repo, that was released on October 18th.
If you use the option available in the "home" menu that pops up when the virtual home button is pressed, there is an option to apply custom screen sizing to the screens of the virtual 3ds. There doesn't seem to be a visible option to keep the aspect ratio of the screens while you are resizing them, making it difficult to keep the correct ratio when adjusting the screen size.