A Jedi doesn't need to see the bolt of energy to be able to deflect it. They would know where it would be via the force.
This can be shown by Luke in A New Hope when he deflects the training droid bolts with the blast visor down.
Watching the films and the rate of fire the Jedi often deal with it would be very unlikely that they use vision at all to deflect the bolts and solely use prescience any way.
Therefore there wouldn't be much use for them to be invisible from a killing Jedi point of view.
Invisible bolts may be useful in an assassin or spy type of role.
I half remember an EU book where there was a rifle that fired invisible bolts that was used to frame Han. I think this was one of the Centrepoint trilogy books. There were Noghri in it.