According to my guide book the mosaics were plastered over by the Ottoman's. In the 19th Century the Sultan had a pair of Italian brothers come to restore the structure, and allowed them to record any mosaics they found before they were covered up again. Atatürk (having turned Hagia Sophia from a mosque into a museum) had an American team undertake restoration, including re exposing some of the mosaics. Not all of them have been exposed. I've got a photo which I haven't processed yet showing Ottoman murals with the faint outline of crosses showing through.

Just come across this on Wikipedia (ah the fount of all knowledge) "a particular challenge arises in the restoration process. The Christian iconographic mosaics are being gradually uncovered. However, in order to do so, important, historic Islamic art would have to be destroyed. Restorers have attempted to maintain a balance between both Christian and Islamic cultures."