By way of example, The Emperor's Gift passage we've heard about is thus:
Emperor's Gift, P124 wrote:On more than one occasion I’d stood with her and her warband in the communal showers after training, blind and numb to any sensation of desire, watching her wash her hair and listening to her speak of serving in the sweltering jungles of Voroxis, killing heretics who spilled from a downed rogue trader vessel.
Bizarrely, the Khatan had declared, upon seeing me wash myself, that my ascension to knighthood was ‘a great shame’. Captain Castor had explained the meaning to me several months later, though I still didn’t see the humour in it.
Of course, the implication most readers get from this is that he has an impressive set of gentials, and the shame is that they are not being used; likewise, however, it is wholly convincing in context that Sosa Khatan's statement refers to the fact that he lacks genitals whatsoever - "it's a great shame that you're a eunuch." In no way whatsoever does it prove that astartes penises exist.
It certainly doesn't disprove the idea that Black Carapace renders the subject entirely without sex organs.