What makes you think that Shinji knows nothing about sex? I mean, he clearly gets that Misato was trying to sleep with him ( I didn't get that the first time I was watching when I was younger).

Also, while anime!Kaworu is rather suggestive, manga!Kaworu doesn't seem to understand human interaction at all (when Asuka call shim a pervert he's confused, he kisses Shinji while he's hyperventilating, etc.)