Both instruments use thermopiles, but the dome over the thermopile determines what kind of radiation passes through and reaches the thermopile. A thermopile is normally protected by a single or double dome to reduce offsets caused by sudden temperature changes like wind.
The CNR 2 uses two glass domes to cover the pyranometer and two silicon domes to cover the pyrgeometers. It uses TWO thermopile detectors (1 for each of the two pyranometers and 1 for each of the two pyrgeometers) and provides two separate outputs. One NETTO for short wave (solar spectrum) and one NETTO for long wave radiation.(Far Infrared spectrum).
So yes, the CNR 2 has separate thermopiles to measure Far Infrared and Solar radiation and so do the other CNR net radiometers.
The detector from the NR Lite(2) is not protected and I sin direct contact with the weather conditions. Therefore it cools down a lot faster by the wind, which effects the accuracy of the measurements. The NR Lite(2) uses NO dome. It uses only TWO detectors with a PTFE coating and provides ONE single output for NETTO short wave- and long wave radiation. It uses one thermopile to measure the full spectrum of Far Infrared and solar radiation.