Certainly after Rei III is created Gendo is much more cold to her than he was to Rei II. Unfortunately for Gendo Rei III carried enough of Rei II within her for Rei III to gain perspective on Gendo's ultimate view of her. Gendo hoped to have his soul along with Adam's body absorbed into Rei's body.
Obviously Rei is naked a lot of the time and Gendo does stick Adam into her through her breast, but I never saw anything in the series that seemed to suggest a sexual relationship. It is known that Rei moved from unwavering loyalty at the beginning of the series to abandoning him for Shinji in the very end, with the consequences that followed. When Gendo tries to merge Adam's Embryo with Rei to start his version of Third Impact, Rei rejects Gendo stating that Shinji needs her from inside EVA Unit 01, and that she is not a puppet of Gendo's any longer. In Rei III's case he sees her as the final piece of his puzzle and as such she's objectified as the means to his end. After Rei rejects Gendo, you see Lilith cup Eva-01 within her hands. Rei would merge with Lilith and proceed to carry out Gendo's directive (which wouldn't have looked all that different from what actually happened). What happened after that is cryptic to me, I'm still trying to piece it together. Like, Gendo Clearly cares deeply about Rei and doesn't want to see her hurt, even if he does hide her away like a dirty little secret but I don't think he was sexually involving himself with her in any way. Gendo and Child Rei. Rei Ayanami's relationship with Gendo is not completely understood and must remain highly speculative, depending on the few shreds of information revealed in the series.
Obviously Rei is naked a lot of the time and Gendo does stick Adam into her through her breast, but I never saw anything in the series that seemed to suggest a sexual relationship. It is known that Rei moved from unwavering loyalty at the beginning of the series to abandoning him for Shinji in the very end, with the consequences that followed. When Gendo tries to merge Adam's Embryo with Rei to start his version of Third Impact, Rei rejects Gendo stating that Shinji needs her from inside EVA Unit 01, and that she is not a puppet of Gendo's any longer. In Rei III's case he sees her as the final piece of his puzzle and as such she's objectified as the means to his end. After Rei rejects Gendo, you see Lilith cup Eva-01 within her hands. Rei would merge with Lilith and proceed to carry out Gendo's directive (which wouldn't have looked all that different from what actually happened). What happened after that is cryptic to me, I'm still trying to piece it together. Like, Gendo Clearly cares deeply about Rei and doesn't want to see her hurt, even if he does hide her away like a dirty little secret but I don't think he was sexually involving himself with her in any way. Gendo and Child Rei. Rei Ayanami's relationship with Gendo is not completely understood and must remain highly speculative, depending on the few shreds of information revealed in the series.