This issue concerns the index iVertex that appears in the CDriver classes, defined in SU2_CFD/src/python_wrapper_structure.cpp (rather, what was formerly SU2_CFD/src/driver_structure.cpp in 5.0.0). Due to iVertex being declared as an unsigned short, one runs into overflow errors when more than 65535 surface nodes are "owned" by a single process (not uncommon for larger models).
Declarations of iVertex as unsigned short may perhaps be more appropriate as unsigned long ?