The two approaches I'm thinking of are
1) One CALayer per dot 2) One CALayer drawing all of the dots
As I use the accelerometer, the dots all change color. I'm using a timer to update the colors, and have overridden drawInContext to draw the current color (interpolation of two colors).
For hundreds, I would draw to one layer (or flip between two) for efficiency. If that isn't smooth enough, OpenGL is the next option to look into.