Actually, Great Houses Indoril and Dres do have holdings in morrowind. You're probably confused because
Morrowind the game actually takes place on the large island of Vvardenfell, which takes up about a third of the province, it's in the north. http://tamrielchronicles.com/assets/concept_morrowind.jpg is a political map of Morrowind.
House Dres is a house built mainly on agriculture and slavery, mostly saltrice. Its plantations and holdings, as you can see on the map, are mostly in the swamps of Southern Morrowind. House Indoril is based on the central mainland, in Mournhold/Almalexia and the outlying cities and towns. Most of the Ordinators on Vvardenfell are of House Indoril. Redoran, Telvanni, and Hlaalu houses all moved their council, main holdings, and leadership to Vvardenfell (with cities remaining on the mainland with less dominance) while Dres and Indoril stayed on the mainland of Morrowind in their plainly-seen capital cities.