There are edible ink pens (I've never used myself so I can't tell you how they work) but I think I would try either black colored icing and a very small round tip or even some piping gel. I'm new to piping gel but what I've read it's good for detailing and writing. Hope that helps :)
The edible food markers work really well. You could also use a round icing tip to cut out little dots of black fondant and attach with a bit of water or meringue powder glue.
I did a lady bug cake that had a little, maybe 3/4 inch size, ladybug on the cake board. I just rolled a little thin line of black fondant for the back and used the small end of an icing tip to cut out tiny little black circles. You could even just roll an itty bitty amount of black fondant between your fingers into a ball and press that flat to make a circle. I liked the icing tip better because they were all the same size and thickness.
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