The primary reason Hypher's so small, comparatively, is that it relies on an externally-loaded jQuery for page integration. Hyphenator.js is completely standalone and thus has to include way more boilerplate for manipulating HTML across browsers. (They even re-implement some jQuery functionality.)
To be fair, Hyphenator.js is a relatively old project that hasn't been completely rewritten along the way to take advantage of substantial browser improvements. (Note that they proudly support Firefox 3.0.) And, more charitably, Hyphenator.js has many more finely-grained settings.
If you're already using jQuery, and don't use Hyphenator.js's advanced API, switching to Hypher may be a worthwhile improvement.