The Belle II experiment at the SuperKEKB accelerator will start to take physics data in 2018. One of the major upgrades of the Belle II detector introduces DEPFET pixel sensors in the two innermost layers of its silicon vertex detector, followed by four layers of silicon strip sensors. Excellent performance of the vertex reconstruction is a crucial ingredient in CP violation measurements and will require reliable and fast alignment procedure and continuous monitoring of the detector performance. To address the possible systematic errors of the procedure, a dedicated study has been performed to identify and evaluate influence of possible random and systematic deformations of the vertex detector on physics observables.