For large HDF datasets it may be better to export the SD that you want using another tool. Then import the raw binary data into Mathematica.

I can suggest the following tool for exporting SD blocks from HDF4 and HDF5 files: 'gdal_translate' is one of the GDAL utilities and works great for this. http://www.gdal.org/frmt_hdf5.html

I am currently working on some code to step through the various dimensions of binary remote sensing files. I am trying to avoid loading the complete file in favor of only loading a single channel, frame, DN value, or spectral profile.

The lower level file I/O routines are your friend there.

Functions of interest are: OpenRead[] Skip[] Read[] Close[]

I did battle with Import[] for a while until it became obvious that I was loading way too much data.

I hope that helps.