I don't know what Hyphenate This does and nothing in my plugin works with it. The option in my plugin adds a CSS file that tells the ACCESS renderer to attempt to hyphenate the text according to it's built-in hyphenation dictionaries. Which are not always so good for even the languages it does support
You would have to ask in the Hyphenate This plugin thread, but if it adds soft hyphens I would expect display problems if you transfer the book as a KePub. I'm not sure how else it could be done though...