hmm - I just checked my TLH (2.4.1-build 160). When I load WAV's, it gives me a choice of APE, FLAC, SHN or MP3. So the option is always there. MKWACT is still up at Etree if you want something just for shn - here is the wiki page...
http://www.etree.org/mkw.html.
Most of the stuff being produced these days is done via FLAC because the developer has ceased working on the software for shorten (if my memory is correct). But, there is no harm done, either way.
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