As Buechsenschuetz said, you shouldn't have any problem as long as you are measuring each one differentially and you do not have any of the batteries referenced to ground.
Even if you did happen to have them referenced to ground you should be okay, because the SCXI-1102B can handle up to +/- 42 V. That figure comes from the
Product Data Sheet. You still can only read voltages up to +/- 10 V, but you could have up to 26 different 1.6 V batteries in series before you damage the device.