The reader's currentWarningLevel is set here.
By default this field is set to UNCOMMON_SYNTAX_WARNING. By setting it to any other facet of NxsWarnLevel you can reduce the number of warnings sent to std::cerr. The warning level is checked in ExceptionRaisingNxsReader::NexusWarn and NxsReader::statusMessage. If the level of the message is greater or equal to the readers level then the message will be sent to std::cerr By calling SetWarningOutputLevel(SUPPRESS_WARNINGS_LEVEL) you can make the reader ignore warnings.