Hall thruster operation is characterized by strong breathing oscillations of the discharge current, the plasma density, the temperature, and the electric field. Probe- and laser-induced fluorescence (LIF) diagnostics were used to measure temporal variations of plasma parameters and the xenon ion velocity distribution function (IVDF) in the near-field plasma plume in regimes with moderate (<18%) external modulations of applied DC discharge voltage at the frequency of the breathing mode. It was shown that the LIF signal collapses while the ion density at the same location is finite. The proposed explanation for this surprising result is based on a strong dependence of the excitation cross-section of metastables on the electron temperature. For large amplitudes of oscillations, the electron temperature at the minimum enters the region of very low cross-section (for the excitation of the xenon ions); thus, significantly reducing the production of metastable ions. Because the residence time of ions in the channel is generally shorter than the time scale of breathing oscillations, the density of the excited ions outside the thruster is low and they cannot be detected. In the range of temperature of oscillations, the ionization cross-section of xenon atoms remains sufficiently large to sustain the discharge. This finding suggests that the commonly used LIF diagnostic of xenon IVDF can be subject to large uncertainties in the regimes with significant oscillations of the electron temperature, or other plasma parameters.