So I suspect that this is actually a "bug" caused by doing things which aren't officially supported and which we have little hope of actually addressing properly. So far as I can determine, Kobo-generated kepubs do not contain soft hyphens and instead use a built-in hyphenation dictionary. I only added hyphenation support because I've never actually seen a hyphenated kepub and most of my books look better with hyphenation. I also don't use centre justification (my settings have it set to "left"). I would say that it's going to be a personal choice, if justification is important then don't hyphenate, or hyphenate and force left justification if hyphenation is more important.
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