The answer to your question is that the Beis Din possessed Dayanim who had medical expertise which they utilized in determining how many blows the criminal was capable of withstanding. This can be learned from the words of the Rambam (Hilchos Sanhedrin 2:1) who writes that only wise and understanding people may be appointed in the Sanhedrin. They must be outstanding in their Torah wisdom and in addition must possess vast knowledge. They must possess a certain amount of knowledge in other wisdoms, aside from Torah scholarship. One of the fields that the Rambam writes that the Dayanim must have some proficiency in is medicine.

The Kesef Mishneh (2:1) cites Ramach who asks why is it necessary for the judges to have medical knowledge? Teshuvas Yehudah Ya'aleh written by Rabbi Yehudah Assad, one of the leading Talmidim of the Chasam Sofer (part 1, Yoreh De'ah #193,) answers that one of the reasons that the Dayanim required some medical knowledge was in order to determine how many Malkus each criminal was strong enough to receive. They would give him a thorough examination and look at his general state of health and natural strength. In addition he writes that the criminal's heart and veins would be checked to see how much suffering he could withstand.

Yehudah Ya'aleh writes that one can infer from two different places in Rambam that they did not employ doctors from outside to do this medical examination but rather used the Dayanim themselves who possessed this knowledge to make this assessment. This can be seen from Rambam Hilchos Sanhedrin 17:1 who writes that the criminal culpable of lashes is struck according to his strength and capability of bearing the punishment. In addition, the Rambam Hilchos Rotze'ach 4:3 writes that if somebody struck his victim with a stone or his fist and he died, one estimates whether the blow was actually strong enough to kill him. (This is based on a Mishnah Sanhedrin bottom 78a). In both instances the Rambam does not state that doctors perform the tests. The conclusion is that the Rambam relied on what he wrote in Hilchos Sanhedrin 2:1 [see above (1)] that the Dayanim themselves have medical expertise so they are capable of doing these tests on their own. The judges do not necessarily have to be experts in all areas of medicine but they must possess expertise in estimating the level of suffering that each person is capable of bearing.

Kol Tuv,

Dovid Bloom