I am currently using USB 6259 DAQ to sample a digital bit-stream with 2Mhz data rate. In the datasheet of USB 6259, however, it says that the digital IO data rate is ~1.25Msps. Does that mean the output data rate of the DAQ or both input and output?
Digital IO means Digital Input/Output and you also need to learn how to read the data sheet. The data sheet states that for Analog Input, the sample rate is 1.25 Ms/s. The max clock rate for Digital I/O is stated at 10 MHz.