Fluxes of neutral particles in the tens-keV energy range are emitted from JET plasmas and measured by a Neutral Particle Analyzer (NPA) close to the plasma mid-plane with the lineof- sight perpendicular to the major axis of the torus. The experimental NPA data on the energy spectra of neutral fluxes allow for validation of both the model for beam ions and that for electron donors in tokamak plasmas. Our study aims at expounding JET NPA measurements of neutral particle fluxes generated by beam ions in a way that lets us conclude on beam ion transport and confinement. Employing both the 3D-Fokker-Planck code FIDIT for fast ions as well as a Monte-Carlo NPA code for bulk neutrals, we model the energy spectra of deuterium neutral fluxes detected by the NPA in JET in the energy range 5keV<E<120keV. The simulation yields good quantitative agreement with the measurements in ICRH-free plasmas. Time-resolved NPA measurements confer useful information about the effect of MHD activity on fast beam ions. To exemplify that we consider a low I/low B JET discharge with a well pronounced NTM and fishbone activity. Analysis and modeling of NPA measurements in this discharge indicate that toroidally trapped fast ions are hardly affected by the modes and that the circulating ions are presumably redistributed or lost by the MHD modes.