Hi,
I'm not aware of any existing tools released by DHI that could do this.
In order to do this you could make a small tool using 1) a library for reading the netcdf files, and 2) the DHI SDK for writing the data into a time varying dfs2 file.
For reading the netcdf files you could use the Gdal open source library (http://www.gdal.org/) for converting each time step in the netcdf file to an ASCII grid file, and then converting the grid files to a time varying dfs2 file using the DHI SDK (see example at http://www.youtube.com/watch?v=q3pfVKRgI6g).
There might be other ways of doing this, but this is one way we have used before.
BR
Oluf (DHI)