Lithium niobate (LNO) is a well established material for surface acoustic wave (SAW) devices including resonators, delay lines and filters. Recently, multi-layer substrates based on LNO thin films have become commercially available. Here, we present a systematic low-temperature study of the performance of SAW devices fabricated on LNO-on-insulator and LNO-on-Silicon substrates and compare them to bulk LNO devices. Our study aims at assessing the performance of these substrates for quantum acoustics, i.e. the integration with superconducting circuits operating in the quantum regime. To this end, we design SAW resonators with a target frequency of 5 GHz and perform experiments at millikelvin temperatures and microwave power levels corresponding to single photons or phonons. The devices are investigated regarding their internal quality factors as a function of the excitation power and temperature, which allows us to characterize and quantify losses and identify the dominating loss mechanism. For the measured devices, fitting the experimental data shows that the quality factors are limited by the coupling of the resonator to a bath of two-level-systems. Our results suggest that SAW devices on thin film LNO on silicon have comparable performance to devices on bulk LNO and are viable for use in SAW-based quantum acoustic devices.