Complex sentence: The Crown had rewarded Nugent generously, and it is difficult to see what he had to gain by treason, though he and his nephew were close, and it is possible that he knew of William's plans, even if he disapproved of them.
Split into simpler sentences: The Crown had rewarded Nugent generously, and it is difficult to see what he had to gain by treason. On the other hand he and his nephew were close, and it is not unlikely that he knew of William's plans, even if he disapproved of them.