I realize that deep sleep should be on the order of < 100 uA, which is below the stated range of the device. However, is it capable of properly computing the integral (i.e., the energy) to bring the measurement into the detectable range of the unit if I was to collect an hour or two of data?
You can measure using DVM in delta (or reference) mode. If the USB meter has such function, then you can probably do as well. The limit is based on the “resolution” of the meter.