ePubCrawler 0.2.4 or higher has an interesting feature: it can find all the hyphenation points in all the words in a document, and convert them to discretionary hyphens in the XHTML output.
ePubCrawler is our ‘work-in-progress’ of a tool for converting InDesign documents to fixed-layout EPUB. More info and download links can be found at https://www.rorohiko.com/epubcrawler.
By default, the feature is turned off. To enable it, open the config.ini file and find the addSoftHyphens setting. It is normally set to 0 (zero). Change this to 1 (one), and then run or re-run ePubCrawler.
Below an extract from a sample XHTML page with both settings.
With addSoftHyphens = 0
<p class="NormalP">With regards to programming styles - I strongly recommend that you copy the programming style used by the InDesign architects. I am fully aware that many people prefer one style over another, but in this case it will make things so much easier if you simply drop your own personal preferences, accept the style, and copy it as-is.</p>
With addSoftHyphens = 1
<p class="NormalP">With re­gards to pro­gramming styles - I strong­ly rec­ommend that you copy the pro­gramming style used by the In­Design ar­chitects. I am ful­ly aware that many peo­ple pre­fer one style over an­other, but in this case it will make things so much eas­ier if you sim­ply drop your own per­sonal pref­erences, ac­cept the style, and copy it as-is.</p>
The text becomes pretty unreadable in XHTML, but the advantage is that you can now easily resize the text frame div in the CSS style sheet and the text will seem to ‘auto-hyphenate’.
It’s not perfect, and text reflow differences between InDesign and EPUB will always make the conversion fraught with pitfalls, but this option gives you another weapon to use when fighting the good fight.