They're sorta doing that for games like Cave Story and La-Mulana (though I don't know if there's any compensation going around for the translations, especially since they received fan-translations years ago). Also they're getting buffed up for release on WiiWare rather than just getting a straight port.
Actually... that also doubles as why they aren't simply doing this for the fan translated game, it's still an amateur effort. Failing all else there would be the lack of creator input pointing out what was done right/wrong, note how games like Final Fantasy V received a much better localization (for its second release anyway) than the fan effort. SE may prefer skipping on a VC release in favor of a proper re-release with a quality translation.
I did not know that they were retranslating it. It sorta disappoints me since I was hopping that by getting the WiiWare version I would be supporting both the creator of the game and the translators + programmer who provided the fan translation. Instead it will just be the creator plus these guys who I'm sure are doing a fine job, but don't provide translations for games that missed their sell by date.