Yeah Yui "died" 10 years before the show's beginning, so there'd be some turnover besides only the science staff would even know her beyond maybe the name, and many of them (like Fuyuiutsuki & ritsuko) are on Gendo's side anyway.
That's more a difference in their personalities though - Generally in their conversations Gendo is the more bold & pragmatic one and Fuyutsuki more reluctant & sentimental but that's reversed when it comes to Rei, with Fuyu once even suggesting that Gendo's getting too attached to her (though that's another difference; Attachment doesn't stop Gendo from using her as planned.) - Chances are Fuyutsuki kept his distance precisely because he felt it's a desacration / is painfully reminded of Yui whereas Gendo's amoral enough not to see a contradiction between seeing her a product of his plotting/mad science AND a kind daughter figure - besides Fuyutsuki never had any kids, unless you buy into that one theory that whole "Yui had an affair" theory that occasionally pops up in fanfic.
Since EVA 01 also sprouts blue hair in EoE I'm inclined to believe that that's related to being created from Lillith.
Obviously they look somewhat alike, as it it repeatedly noted but even "strong resemblance" doesn't equate identical. It's interesting that when we first see Baby!Rei Gendo's decked her out in the same hairstyle Yui had but later on Rei has it slightly shorter & messier and doesn't bother to get it out of her forehead. Like she roughly stuck with it ever since but as a simple consequence of doing it herself eventually & not knowing the "template" she subtly adapted it to her own low-maintenance, bare-functionality style though the texture is still notably different with how both have it fall onto their cheeks like that -
As I've read Sadamoto was going for a "wolf-like" , semi-messy/low maintenance style with the hair.