Regarding this kind of topic, what you should ask yourself is not, "would I be okay with a Zelda reference being in this CoC mod?" (the answer is "it's probably like a quarter as influential as Lord of the Rings ever was at this point as far as pop culture is concerned. It's fine. Deal with it.")
Rather, the question to ask yourself is, "is this specific plot point used for goblins actually interesting on its own merits?" Basically, nobody should give a fuck if it's a reference or not. Does it fit the goblinoids' vibe and identity? As far as I'm concerned, goblins usually have some kind of shamanistic culture, and I think the idea of men being born to them only once in a blue moon fits the vibe. They need some "cultural lore" for that, so it fits the mentality. They're a grubby little race of fucksluts with fat asses that only sometimes veer into the realm of "comically smart/capable" (Lumi, the assassins, etc.). A race like that doesn't just spawn naturally. It's utterly ridiculous on its face. They would immediately get absorbed into any other dominant culture nearby or get wiped out. They lack the pride and tradition of the Gerudo, to say nothing of their lack of physical strength and stature.
Therefore, I think the idea of a goblin prince of immense power gives them some kind of cultural center of gravity to keep the race a bit more sensible and grounded. Plus it would be REALLY hot to forcibly turn him into a girl and completely shit all over goblin culture, breaking an eons-long cycle by absorbing him into my ever-growing harem of exclusively women.