Absolutely. Multithreading is encouraged!! The FrontPanel Application itself is multithreaded. Our EVB100X okCameraApp is also multithreaded to read camera data and display in separate threads. Otherwise, the GUI message queue would make things very uncomfortable for the user.
But as you mention, you need to mutex the access to each device. You can have multiple devices open in multiple threads and accessed simultaneously. But accesses to any one particular device must not overlap.