The black beads appear to be bolder than any other colour beads. The hole in the middle of the beads appears black, so black beads appear solid.
Outlines should also be designed differently. Usually your background is at the same resolution as your artwork, but in the case of beads your background has an almost infinite resolution, and many more colours.
To me the goomba in Seiseki's image looks the best as it has no outline at all. Though against a different backdrop that could change.
So if you have a choice, I'd change the outlines a little, or possibly even remove them. That said, any pixel art that has been beaded still looks pretty awesome.