You are not looking for a breakout board if you are wanting it to be USB. There are several controllers that connect via USB, the SmoothStepper USB and the Kflop are the two I can think of. They are both motion controllers.
There is also the PoKeys 56U which is a 55 I/O device that can accept up to 3 fast encoder inputs but you can connect many PoKeys, or rather will be able to when the plugin Brian is currently working on becomes freely available. That would allow you to have 6 encoder inputs, you can also write these inputs to user DROs so the 3 encoder input limitation of Mach is not a concern.
I am not sure if the pokeys will be able to use a probe input but the others can as far as I am aware.
I dont thnk the SmoothSteppers encoder inputs will be fast enough for high count/high speed encoder inputs but likely would be fine for lower resolution encoders.
I have been testing the Pokeys 56E (Ethernet version) with encoders and have it connected to the output from a servo drive, the motor is 4000rpm max and encoder is 2000line (8000 pulses per rev) so that equates to 533KHz and it has not lost a single count on the multi millions it has received in my testing.
I have not tried it with more than one encoder to date but will be trying in the future as I test the plugin as Brian develops it.
I have also been testing the PoKeys 56U with encoder inputs and it does seem to lose a few counts but not many over the millions it has received. I know they are looking right now to see why that would be and may be cured shortly.
Hood