Well... so, I am reading leviatan scans' legend of the nine suns. the first chapter contains a lot of censored words, thus my mind tries to come up with (in)appropriate word to fill those. Then, after looking at the bunny (girl) boy dress that the protagonist wore, I suddenly feel like having the desire to see a neutered MC. I'm not looking for MC with erectile dysfunction, but literally got his junk cut. Not looking for yaoi though.
Not exactly what you're looking for but this is the closest I know of: Smiling Proud Wanderer The Sunflower Manual in the story is very famous that it's mention in many works.
You want to read a story about a eunuch? None come to mind. In " The Marquis of the Grand Xia " the protagonist almost became one in the first few chapters and for the rest of the story he had to pretend he was one, but he didn't actually become one.
It kinda impossible to find The closer i found is Arifureta where Yue destroy the ball of nasty men literally (a lot of them) and one of them change name into crystabell something and later make ??? group, however crystabell something is not MC There is short story (CN i think) about a man named Gu(???) that have massive big d*ck, he has a wife and one day when they home, they forgot the key so the wife climb the d*ck and Gu(???) able to lift her into window to slip in the house. Later in the next episode of their happy family life, earthquake happen and make the wall fall into the wife, the husband want to help but obstructed by his big d*ck (he cannot reach his wife) and wife died. Very sad so he decided to cut his d*ck, the story end after he really cut it. I got this short novel from this forum 2 or 3 years ago........
if you're okay with manga: Anorexia - Shikabane Hanako wa Kyoshokushou https://www.mangaupdates.com/showtopic.php?page=1&tid=23297
There is this novel? that the premise is lesbian feminasties couple got a boy and they hated him because he is male, so he cut off his junk and went to find his biological father.....messed up so I didn't remembering anything more. It is similar to "A thousand league in search of mother" but this time it is father. I seen it on a dead raw site and it is not translated as far as I know.