All transformative fandom (fanfiction, fanart, speculative meta) involves some extrapolation from canon; otherwise, we're talking about curatorial fandom (Star Trek folks out there counting how many doors we see on the USS Enterprise during each series run, Silmarillionheads charting the lineages of elves back to the dawn of time, etc.)
This means that if you're in transformative fandom, "canon vs fanon" isn't a binary, but a spectrum.
YGO is an interesting case because there's a zillion canons to pull from, all of which both reinforce and contradict each other constantly. Also, much of the fandom has been kicking around for 20+ years, mixing and matching at will; the horse is out of the gate, and trying to enforce strict delineation between anime/manga/spinoff films/filler/dub/sub/etc on the entire fandom is a lost cause. I think that's actually even more of a reason to add in some nuance and work off a spectrum, because in a canon this (I say lovingly) convoluted, there's some real value in being able to broaden your evaluation tools past "canon vs. non-canon" and figure out which bits of 'fanon' might actually trace back somewhere.
Here's the rubric I tend to work off:
"Honda Hiroto attends Domino High School" - this is stated canon. It is a declared fact in-story, and there are no conflicts across any Yu-Gi-Oh! medias.
"Honda is loyal and conscientious" - this is directly conveyed canon. Honda is demonstrably loyal to Jounouchi and later to Yuugi. Honda carries and looks after people when they're incapacitated. Honda makes sure people aren't left behind: he advocates for the Kaiba brothers in Duelist Kingdom despite his personal distaste, and he checks up on Bakura more than anyone else. This is a major character trait and you're clearly meant to get this out of the source.
"Honda is interested in machinery" - this can be reasonably inferred from canon. Honda rides a motorcycle, is frequently associated with mechanical imagery in the context of Duel Monsters, and is seen in DSOD repairing Jounouchi's duel disk. It's not the major focus of his character, but it's still a straight line you can draw from canon.
"Honda really fucking likes cantaloupes" - this is esoteric canon. It is mentioned Once in capsule monsters, and literally never again. This could easily be confused for fanon, but...it is indisputably canon. to something.
"Honda would become a mechanic post-canon" - this is grounded fanon. Despite his interests, Honda never actually mentions wanting to be a mechanic. While he does mention that he's expected to work at his father's factory post-graduation, he's clearly not thrilled about it. Because the series ends before we see what he actually chooses, there's nothing directly supporting or contradicting this fanon; but it also doesn't come out of absolutely nowhere.
"Honda has asthma" - this is ungrounded fanon. I give Honda asthma in my personal headcanons because I have asthma, and I love Honda and relate to him and want to project my shitty lungs onto him. There is absolutely nothing in canon to suggest this. If you wanted, you could argue with me and tell me that this is a ridiculous headcanon. It would be unnecessarily confrontational, but you'd be correct. And if I were to go around telling people they were stupid for not making Honda asthmatic, I'd be both unnecessarily confrontational and wrong.
There are definitely some medias where it's really easy to suss out when the fandom is just running with some randomly invented fanon that has inexplicably replaced canon. Unfortunately yugioh is not one of them. but...that also means you get to enjoy the delight of explaining to people that Yami Alexander the Great and Henry Tudor Yugi are not mass-hallucinated fanon AUs, but both actual (and completely unrelated) canon.
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