So I thought I needed command-line support (ironically, I was wrong -- I wanted to add hyphenation to autodownloaded periodicals, but of course periodicals only work in MOBI format and discretionary hyphens are only supported by the AZW3 reader -- thanks, Amazon).
So I wrote it. Only halfwitted for now, specifically it only uses the configuration you set from the GUI (you cannot set your own) and it always uses only the English dictionary, though fixing the latter should be a trivial argparse away. But it works, or appears to.
Patch is here:
http://www.esperi.org.uk/~nix/ht-0.0.8-hyphenation.diff