It was not possible to identify lithium an nitrogen. What is the effect of the Be window in this case? Can this be explained with the K-Shell of nitrogen?
It depends on the thickness of the Be window. Those low-energy x-rays are strongly absorbed in the window, so if it is thick, the intensity of those x-ray lines in the spectrum will be small. This means the detection efficiency is low.
Usually it is convenient to look at the specifications given by the manufacturer of the detector.