It is certainly possible, if you’re willing to build your own custom fixtures to hold the spheres. The egg holders that come with the EggBot are designed for objects above a certain size. Issue (1) is that they don’t reach far enough to touch each other– you’ll need to extend both, in order to fit arbitrarily small objects. Issue (2) is that the egg holders have a certain diameter, which (while appropriate for larger objects) will obscure quite a bit of a small sphere.
All of the software and motion control will essentially work fine for you, but you do need to worry about those two issues, and you may well be able to adapt it to work for you.