Update netcdf-java and revert NetcdfFile opening changes

[melissalinkert]

I assume there is an outstanding TODO of reverting this workaround once we have a new upstream release of netcdf-java with the bug fix. Is that better captured as an inline comment or a dedicated GitHub issue?

Originally posted by @sbesson in #4409 (review)

[melissalinkert]

Once a release that includes Unidata/netcdf-java#1492 is available, we should be able to upgrade and then revert #4409.