Rei isn't afraid of being replaced, she knows she's replaceable and has resigned herself to that fate.
Those two things don't neccessarily contradict each other - She may have accepted it as an unchanging fact of life and still feel aun unpleasant tug in the pit of her stomach when she contemplates the thought
I mean, she doesn't just do what people tell her because she has no thoughts of her own (unless we're strictly talking of her 3.0 version). When Shinji questions Gendo her response is not to say "Why would you say that?" or "The commander is always right.", but to get mad and sock him in the face
because how dare he.
She's more like a cult member (a comparision Anno explicitly made once IIRC) than a robot - she truly believes in Gendo's plan since she's been brought up in isolation with her whole life focussed on this big external mission, that her life, her thoughts and her feelings (which she very much had since the beginning) are unimportant compared to The Cause and that she has, can't have, nothing outside of it, something that is certainly exaggerated/emphasized by how Gendo can just warm up a new one of her at any time.
Asuka certainly assumed that, as she puts in in ep 11, "she would do anything to get her goal", but it's telling that when she's actually ordered to do something that could be considered ruthless or dicey, she reacts very differently, such as when she questions Misato's orders to retreat after Shinji gets swallowed by Leliel, or when she gets steamrolled by Bardiel because she had real difficulty blasting a classmate whom she had a few vaguely friendly interactions with, not to mention that she consistently displays the most care for her comrades out of the three pilots (ste stays at Shinji's bedside after Ramiel grilled him way before they were actually friends, and even tried to give Asuka
And not minding if people see her naked probably has less to do with "submissiveness" and more with being raised in isolation away from human condition as a lab specimen that probably gets poked and prodded all the time, Ritsuko, Fuyutsuki and Gendo have dry technical business conversations all the time while she just stands there in her tube. She's probably read enough biology books to know what humans do with their dangly bits but it doesn't pertain to her since its not In The Plan.
That would probably have quite the opposite
effect on any potential sexual encounters she might have in some hypothetical future.
There's nothing "special" about being naked for her and she probably has a rather distant relationship to her physicality - in some sense her body is a swappable part of hardware somewhat 'mismatched' to the Lillith-derived software, besides, it's some frankensteinesque device that Gendo made as a remote control for Lillith and third impact, with a dead woman's face to boot, a meat-machine owned and mantained by NERV at best and at worst a cumbersome conduit through which to experience pain. Heck, she probably has a sorta abstract, in-her-head bookish personality to begin with, even before all the other stuff is taken into account.
We've seen that she certainly has the capacity to yearn for an intimate, primal sort of connection, but I could easily see her having difficulty connecting that or getting that in some sort of alignment with vaguely tingly sensations in the downstairs regions.
While its certainly possible that she could eventually learn to see her body as a vehicle for pleasure and self expression (and that this might well turn out to be a transformative experience, in the same way that learning to value the simple earthy pleasures of yummy nom stuff and to make a social activity out of it was imho legit positive development in the rebuilds), I doubt she'dfind a lot of enjoyment in , or even be particularly good at
the bottom position or passive role, you'd probably have what certain men crudely term 'dead fish syndrome' until she had some time to get in tune with her body.
I mean there's a couple of situation where she does display a capacity for embrassment (such as when Shinji tries to refashion his Yui-related shower thought into a compliment) or "!! my stuff !!" (look at her expression when she comes home during Touji and Shinji's visit, but before the latter explains that he touched nothing other than the trash), but there's very, very little that qualifies as "my stuff" in Rei's world, not even the meatsack she lives in, and there is certainly some perversity to that