We have carried out a detailed analysis of highly ionized neon spectra collected at the NIST EBIT using an NTD germanium X-ray microcalorimeter developed at the Harvard-Smithsonian Center for Astrophysics [Nucl. Instr. and Meth. A 444 (2000) 156]. Our attention was focused especially on the Ne IX He-like triplet to check electron density diagnostics through the intercombination/forbidden line ratio. We have investigated possible effects of the ion dynamics on the plasma emission line intensities, looking at the dependence of the count-rate and the charge state distribution on the electron beam energy and current. The temperature and spatial distribution of the neon ions, and hence the overlap between the electron beam and the ion cloud, depend on the electron beam operating parameters. The overlap affects the average electron density seen by the ions, and in turn the measured line ratio. These results underscore the value of future improved studies of the trapped ion dynamics, both for understanding the EBIT performance and for allowing experimenters to take full advantage of its potential for astrophysical plasma diagnostics.