We do use some pictures of a board without a header on the product page, but the #3117 RPi bridge has the 2x20 pin female header soldered in and comes with standoffs, nuts, and screws that allow it to mount as a Raspberry Pi HAT. We also sell a variety of other 0.1" headers separately that can be soldered into other locations on the board. By the way, if you do not want the 2x20 pin Raspberry Pi connector, we sell a version of the board with only the SMT components.
The Zumo chassis kit you mentioned should work with those encoders. There are slots in the acrylic plate that allow enough clearance for the encoders to sit and allow the headers to be accessed.
There should be enough interrupts available on the A-Star 32U4 robot controller to use the encoders. INT0 and INT1 will be taken if you are using a Raspberry Pi and PCINT5 and PCINT6 will be taken if you are using both motor channels, but the other interrupts could be accessible if you are not using the functionality on those pins. We do not have example code for these encoders, but the A-Star 32U4 uses the same microcontroller as the Arduino Leonardo and Arduino Micro and there is an Arduino encoder page with a lot of resources that should be helpful for you.