Scholars agree that the Beautiful Names of Allah are not limited to 99 names. The hadith: Allah has 99 names, etc., does not mean that Allah does not have any names apart from these, rather it means that whoever learns these 99 of His names will enter Paradise.

Allah being above His Throne and above all of His creation means that He is above all creation. He is above heaven, above Paradise, above the Throne, and none of His creation encompasses Him, and He does not need any of them; rather He is their Creator and Sustainer.