Supernova remnants (SNRs) are believed to be the major contributors to Galactic cosmic rays. The detection of non-thermal emission from SNRs demonstrates the presence of energetic particles, but direct signatures of protons and other ions remain elusive. If these particles receive a sizeable fraction of the explosion energy, the morphological and spectral evolution of the SNR must be modified. To assess this, we run 3D hydrodynamic simulations of a remnant coupled with a non-linear acceleration model. We obtain the time-dependent evolution of the shocked structure, impacted by the Rayleigh-Taylor hydrodynamic instabilities at the contact discontinuity and by the back-reaction of particles at the forward shock. We then compute the progressive temperature equilibration and non-equilibrium ionization state of the plasma, and its thermal emission in each cell. This allows us to produce the first realistic synthetic maps of the projected X-ray emission from the SNR. Plasma conditions (temperature, ionization age) can vary widely over the projected surface of the SNR, especially between the ejecta and the ambient medium owing to their different composition. This demonstrates the need for spatially-resolved spectroscopy. We find that the integrated emission is reduced with particle back-reaction, with the effect being more significant for the highest photon energies. Therefore different energy bands, corresponding to different emitting elements, probe different levels of the impact of particle acceleration. Our work provides a framework for the interpretation of SNR observations with current X-ray missions (Chandra, XMM-Newton, Suzaku) and with upcoming X-ray missions (such as Astro-H).