NetCDF should not be limiting the number of variables. It does limit each variable to less than 4GB in size and also the total number of records in the entire file to be less than 2^32 (this is to maintain 32-bit support for the format). Do you know if you are hitting the record limit or file size limit? Either way, IDL's NetCDF libraries have been updated in the last few years to be more current. IDL 8.8.1 ships with the NetCDF C library 4.7.1 which may help with this issue.