The accurate simulation of vibrational energy transport and quantum thermodynamics with trapped ions requires good methods for the estimation of temperatures. One valuable tool with this purpose is based on the fit of dark resonances in the fluorescence spectrum; however, the reliability of this technique remains uncertain. In this work, we evaluate several simplified dynamical equations for simulating the spectrum of a trapped ion undergoing thermal motion, highlighting the strengths and limitations of each method. Additionally, we analyze the applicability of this approach to measure local temperatures in a chain of trapped ions. Our study includes a detailed experimental proposal for measuring non-equilibrium profiles of the effective temperatures in this system, supported by numerical simulations of the dynamics and the measurement process.