The CDAWeb data source assumes that data references in the all.xml database are all CDF files, and culls the entries which are not. More data is entering CDAWeb that is NetCDF, and this should be supported. The CDAWeb source delegates to the CDF data source, so it should be a fairly simple task to make it delegate to the NetCDF data source in this case as well.
There are formosat files which demo this: see FORMOSAT5_AIP_IDN in all.xml.
I've verified that Autoplot can read and use these NetCDF files. Note there are others which will require an upgrade to the NetCDF library I use.
Bernie points out that the master which modifies the file is CDF.
See also https://sourceforge.net/p/autoplot/bugs/2191/ which talks about the NetCDF version problem.