The menus basically just use the "menu" font built into Decker. It is possible to edit this font or the other built-in fonts (using for example the editor in the example fonts.deck) and these changes will be saved along with the deck.
If you've got a separate Decker font and want to use it to replace the default fonts, I'd assume this is possible somehow but I'm not sure the best way to do it.
Although if it's eyestrain that's the issue, it could be worth looking into changing the palette instead?