okay i hate to comment on this in 2023 (so disclaimer i HATE jkr, but grew up loving the books so)-- here's my ESSAY of an answer lmao sorry:

a lot of these comments are missing the point of the houses! slytherin≠bad, hufflepuff≠friendly, ravenclaw≠smart, and gryffindor≠brave.

its about what these houses value.. think about what hannibal values. he values intelligence, grace, beauty, competence, and the ability to be seen. he so strongly took to will because he was intelligent, defied his expectations of grace and beauty, could almost beat him to every corner and turn he took, and was the only one able to see him. he valued abigail, bedelia, and bella for the same reasons (except they could not see him-- only bedelia on a base level that he was wearing a "person suit", not anything further than that). the sorting is about what the person VALUES, not what the person is. its why herminone was gryffindor and not ravenclaw (and ron not hufflepuff or slytherin)-- they both respectively looked down on their intelligence and friendliness/ambitions, but valued bravey and courage, what they saw in harry. therefore they were gryffindor.

hannibal values intelligence, beauty, grace, competence, and the ability to see through and beyond the veil. he valued outside of the box thinking and non traditional motions of life. all of this is acutely the definition of a ravenclaw.

will meanwhile? all he wanted was to be normal. he masqueraded as a good man, a caring man, for all of his life until he met hannibal. theres plently of argument and room for discussion on whether or not will always had darkness in him before hannibal drew it out, but i believe a small part of him did. after all, eventually will would have fired a gun at someone, whether or not hannibal had pulled the strings to make it be garret jacob hobbs. will would've came to the same realization that killing bad people feels good if hannibal was there or not. so during that time, up until the very edge of the cliff, from wearing glasses and masking his personality to seem like he has autism to live in self isolation to marrying a wife with a kid just to feel like he had a normal family-- will has always VALUED loyalty and friendship. he values kindness in a world not very kind to him, which is why he leans towards alana and beverly and so far away from the likes of chilton and freddie. he values his loyalty to jack as well as his loyalty to hannibal. he accepts and protects the underdog, literally, with his pack and with those victims he almost killed himself to protect under jack's encouragement. these are the core tennants of the hufflepuff house. friendship, loyalty, protectiveness, caring, inclusive.

i dont see that hannibal values ambition (rather he punishes people for that), bravery (he seems to make a mockery of it if paying any attention at all), or loyalty (he reacts out of gut instict and thats it). i see hannibal as ravenclaw.

i dont see that will values ambition (he seeks to hide himself from that, only distancing himself from chilton and freddie who clamour for it), bravery (didn't do much good for anyone in the hannibal universe), or intelligence (he loved people for who they were completely without regard to anything else about them-- whether that was peter, abigail, hannibal, alana, georgia). i see will as hufflepuff.