The footnotes to the wikipedia article on Leonardo provide references for the sodomy arrest and the allegations regarding his apprentices.
You make a good point, though; Leonardo does seem kind of asexual. It’s certainly possible that his aesthetic choices were not his sexual choices.
I see that reference in SunkenCiv’s post above yours. I see that it mentions the accusation was anonymous which corresponds to what I read about a system of “accusation boxes” put up in Florence. (I mistakenly said Milan before forgetting where he lived for most of his life while in Italy.) I also note that he was exonerated based on lack of evidence. If they couldn’t find it then I doubt that anyone will find any now.
I don't think anyone can doubt that he had an eye for the beauty of structure whether that of living things or inanimate things. He created a huge body of work on war machines, some of which are still inspiring technology today, and yet he hated war.
I think he loved his mind and he loved to work and he primarily produced what his patrons paid him to produce. He had a very poor opinion of humanity in general. I think he wrote that most people contribute nothing to life but consuming food and producing feces.
If he had a special fondness for his apprentices it was probably because they loved the work he was doing. They probably had to work very hard to keep from being shown the door. I suspect that hard work and talent were the only things he respected.