Dark mode affects the colour of the menus and inspector but it won’t change the colour of the board or the text, since these are customisable and we don’t want Scapple messing up what you’ve already set. But by the same token, you can both change existing boards and set dark defaults for new boards.
If you open View ▸ Inspector and scroll to the bottom of that sidebar, you’ll see the Document Settings, which include the default board colour and the default text colour (clear this to leave it uncoloured and dynamically adjusting to the background). These settings will affect the current board, but you can also then click the Set as Defaults button there to, surprise surprise, set them as the defaults for new boards you create. You can also create custom note styles appropriate for a dark mode and then set those as defaults via the Styles tab in File ▸ Options.
As an example, or to use for yourself, there’s a dark theme board here which you could download and then use to set the defaults, or just inspire you for your own design. 