A further update, the Arch Linux AUR package is now building HDFView 3.1 successfully. I'm using it on Arch and it works. If Debian wants to replicate this for their package, see the build script here: https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=hdfview
The AUR package patches HDFview's build.xml file to unbundle java from the resulting package and to remove what looks like a workaround for incorrect library filenames that is not relevant on Arch. This may or may not be identical on Debian, but may be a useful starting point for anyone wanting to solve this bug.
