Is it a good idea to chisel out the edge of rafters for wires?
The top or bottom edges of a beam are the worst places to cut. It is where the most stress occurs. This is one of the reasons why it is best to run wiring/plumbing through holes in the center of your beams. Will it cause a problem? That is impossible to know, unless we also knew how much of a load you would be adding up there, the dimensions of these beams, etc.

While it is very possible there would be no problem, remember that those rafters were put there with no plans for a floor above. The structure may not have been designed to take a load. So if these are 2x4 rafters, on which you will then install a waterbed or a hot tub, expect problems. If you will be just using that floor to store a few light boxes, it probably won't be an issue.

If the floor that you add consists of 4x8 sheets of plywood, they will add considerable stiffness to the floor, but they will also add weight. As an alternative, you might consider adding sleepers on top of the rafters, which would allow you to avoid cutting into these members at all.

Finally, remember to be very careful in nailing/screwing down the new floor. A nail through an electrical line tends to be bad news.