There *is* a potential workaround if the USB version of the card supports change detection on Port 0 of its digital inputs like the PCI version of the card.
You would set up a dummy continuous DI task using the "Change Detection" version of DAQmx Timing. You'd have to specify which edges of which lines to detect changes on and also physically wire the signals of interest into digital lines on Port 0 of your card. Finally, your counter task that measures the encoder would need to use an internal signal named something like "DevN/ChangeDetectEvent" as its sample clock.
I've used this kind of technique to sample various stuff in sync with encoder quadrature state change. Here's a posted example that may help too.