I found what maybe the perfect journal article that addresses your question: McNeill, John T. “Natural Law in the Teaching of the Reformers.” The Journal of Religion, vol. 26, no. 3, 1946, pp. 168–182. A copy can be found at JSTOR. Its 15 pages are divided into 4 sections treating Luther, Melanchthon, Zwingli, and Calvin individually.
I believe the Reformers's issue with Aquinas and the scholastic theologians in general, is about natural theology, not natural law, since the Reformers believed that the Medieval approach to Christian theology was too much influenced by Aristotle that the scriptural interpretation has been compromised. This is part of the larger humanistic enterprise which called for Ad fontes ("to the sources") not only to classical Latin (for humanists like Erasmus) but also for the Reformers going back to the Hebrew and Greek manuscripts as opposed to relying on the Latin translation for the Bible.
I share the observation of the OP and lament the fact that Protestants rarely use Natural Law reasoning when it comes to defining their Christian position on controversial ethical topics of today. While the article doesn't directly treat why this happened, many citations of the Reformers's writing on their understanding of natural law may point to the Reformers's distrust on using reason for moral argument since they believed reason itself has been compromised by sin. Thus they severely restricted the application of natural law reasoning to minor duties, one of which was to explain why pagans could behave justly even without revelation (answer: because even after the Fall there are still traces of natural law which is implanted by God into human hearts). This then forced them to rely more on scriptural arguments. I'm sure they couldn't have anticipated how Bible authority has been severely diminished 500 years later, and Christians need all the help they can from Christian and non-Christian philosophers alike who still cling to the belief of objective morality, just like how Plato and Aristotle reacted very severely to the Sophists who deny that there is an objective basis of morality.
As another poster already pointed out, the Reformers didn't mention Summa Theologica in their writings, so the article also doesn't mention the Reformers's position on the Summa. Again, I lament that Protestants don't make use of the excellent treatment of virtues, vices, and human nature in the Summa. It looks like the trend has started all the way since the Reformers's own period, and maybe due to the SAME distrust of Aristotle I mentioned above. The critical element of Aquinas's theory of virtues is Aristotle's Final Cause, but with the pre-modern scientists ALREADY reacted negatively to Aristotle's Final Cause, probably the Reformers were loath to use Final Cause in the areas of moral reasoning as well, although now Final Cause even in the area of science is beginning to make a comeback. Without Final Cause, it is no wonder that the Reformers wouldn't use natural law argument either because Final Cause is the most important element of natural law argument. In the modern period, natural law begun to be redefined beyond recognition since the Final Cause element was thrown out, which reduces today's applicability even more. If we were to bring back natural law argument, we will need to restore respectability to the Final Cause element FIRST. Excellent treatment of the historical development of natural law can be found in the Teaching Company's Great Course on "Natural Law and Human Nature"
Below is the first paragraph of the article:
THERE is no real discontinuity between the teaching of the Reformers and that of their predecessors with respect to natural law. Not one of the leaders of the Reformation assails the principle. Instead, with the possible exception of Zwingli, they all on occasion express a quite ungrudging respect for the moral law naturally implanted in the human heart and seek to
inculcate this attitude in their readers. Natural law is not one of the issues on which they bring the Scholastics under criticism. With safeguards of their primary doctrines but without conscious
resistance on their part, natural law enters into the framework of their thought and is an assumption of their political and social teaching. This is assuredly not a consequence of what we may all the" active" element of their theology, which denies independent value to good works in the realm of salvation and throws into relief man's sin and God's supernatural grace. The seeming
incongruity here is not our present problem. The assumption of some contemporary theologians that natural law has no place in the company of Reformation theology cannot be allowed to govern historical inquiry or to lead us to ignore, minimize, or evacuate of reality, the positive utterances on natural law scattered through the works of the Reformers. The bearing of natural law upon theology in these writings still calls for clarification. In this study we must observe a rigid economy, which excludes all that is peripheral to our special topic and, therewith, much that is important for the history of theology. But reference to some points in the area of contact is unavoidable.