Pope Paul III's encyclical of 1537, Sublimus Dei , never addressed the topic of whether or not the Indians had "souls" but whether or not they were "dumb brutes" fit only for slavery.
In other words, the question in Spanish conquered territories at the time was whether or not Indian in the 1530's should be treated as blacks were treated in the U.S. in 1830.
It is a fact that Spanish adventurers saw the Indian population as a source of profit.
However, as far as the Spanish Crown was concerned, the Indians were Spanish subjects and their fair treatment was addressed not only in the last will and testament of Queen Isabella but also in the Laws of Burgos of 1512 which specifically commanded that they should be given Christian instruction.
Queen Isabella, in particular, always considered the Indians as her royal subjects and not "subhumans".
Sublimus Dei is a papal bull promulgated by Pope Paul III on May 29, 1537, which forbids the enslavement of the indigenous peoples of the Americas and all other people. The pope used in the bull almost the same language as in his letter, Veritas ipsa, to Cardinal Juan de Tavera, Archbishop of Toledo, sent less than a month earlier on May 2, 1537. In these, Paul III unequivocally declares in his language declaring Indians to have souls and be included in those God had endowed with capacity to attain to the inaccessible and invisible Supreme Good and behold it face to face. Thus the indigenous peoples of the Americas were rational beings with souls, denouncing any idea to the contrary as directly inspired by the "enemy of the human race" (Satan). He goes on to condemn their reduction to slavery in the strongest terms, declaring it null and void for as well as for any people known or that could be discovered in the future, entitles their right to liberty and property, and concludes with a call for their evangelization.