van der Waals metal chalcogen thiophosphates have drawn elevated interest for diverse applications, including energy harvesting, electronics and optoelectronics. Despite this progress, the role of nanoscale ion migration in complex intermediary thiophosphate compounds has not been well understood, resulting in their structure-property characteristics remaining elusive. Herein, we focus on copper-deficient CuCrInP₂S₆ as a prototypic layered thiophosphate compound to address this shortcoming. Piezo force microscopy reveals that this material exhibits unusual cage-like domain networks with an enhanced piezo response at the domain boundaries. The associated piezoelectric coefficient d₃₃ is found to be among the highest across reported van der Waals multi-layered materials. These results are further complemented with Kelvin probe microscopy and second harmonic generation spectroscopy that disclose significantly elevated non-linear optical emission along these domain boundaries. Ab initio calculations performed in conjunction with nudge elastic theory provide a deeper insight into the diffusion processes responsible for these observed phenomena. These findings shed new light into intermediary thiophosphate based 2D compounds, highlighting future prospects towards their use in emergent piezoelectric based technological applications.