I confirm what others have stated - gills should be left on Shitakes, whether you're using soaked dried or fresh, but the stems, which are tough, should be removed, although you can save them for use in making stock if you wish.
In fact, a basic rule to keep in mind if you're not sure about the mushroom gill situation, especially since there are so many fresh exotic mushrooms on the market these days is that light gills can always stay; dark ones can be removed at your option.
Unless I'm stuffing a mushroom with something, I usually leave the gills in regardless of color. But again, that's just my preference.