I have a yun board and a motor shield, with two motors. I have encoder for pololu wheel 42x19 mm, just for the A motor, in order to test.
I have downloaded libpololu-avr library and copied PololuWheelEncoders, OrangutanResources and OrangutanDigital diretories to Arduino\libraries.
I have written the simple code:
Unfortunately, the PololuWheelEncoder library does not work with the Yun. However, you should be able to read those boards with other encoder libraries that work with the Yun.
Dou you know wether it is posible to read encoder inputs signal without using attachInterrup function, because signals are very fast sent, and Arduino cannot read all of them?
Unfortunately, I do not know where you can find encoder libraries for the Yun. However, using encoders is common in robotics, so I expect them to be available online.
Generally, interrupts are used because encoder counts need to be read quickly, but if you do not need to read encoder counts very often, you probably do not need to use the interrupts.