Multifunction DAQ cards from National Instruments (X Series, M Series, E Series, and Compact DAQ) can take differential samples at their maximum rate on a single channel. This is because the card internally routes different signals to the ADC. This table is an example to show a comparison on the PCIe-6353:
Figure 1) X Series AI measurement type example for AI0 on the PCIe-6353
In the case of a differential measurement, the card routes the analog input channels to the positive and negative terminals of the ADC, making it a true differential measurement.
On the other hand, when measuring multiple channels, whether they are single-ended or differential, the signals are multiplexed into a single ADC. This causes the effective per-channel sample rate to be the maximum aggregate sample rate of the card divided by the number of channels.
S Series devices are built on a multiple analog-to-digital converter architecture, so there is no aggregate sampling rate between all of the input channels. You should have no issues sampling at the maximum sampling rate defined by the hardware.