Solution
Yes, the NI-9401 module can acquire two channels with different rates in FPGA Mode since it is part of the "on-demand sampling" group of modules, which means that a sample is taken when reading from the module using an IO node. The sampling rate is controlled by setting the speed of the cycle in which the IO node is read. This can be achieved as long as you aren't trying to read faster than the specifications of NI-9401 (e.g. with two channels is 20 MHz each).
The snapshot shows a way to acquire digital input from DIO0 and DIO4 at different rates, respectively 2 kHz and 4 kHz.
