In retrospect, it's so obvious he's almost ashamed of himself for failing to notice before. In his defence he has to say he's always at a disadvantage when sex is involved, because while he's not alarmed by it he can't quite grasp the main points either.
And yet the signs were all there, as plain as the nose on his face. Molly's obliviousness to the fact that 'Jim' was posing as a gay man, and her general awkwardness around potential romantic partners; even the out-of-line remark about her 'having quite a lot of sex' with Tom, which threw him out of scent back then, was nothing but a broad hint in the right direction.
"You shouldn't hide it, you know," he tells her without preamble as she strolls into the morgue, and she almost drops the Styrofoam cup she's holding.
"Sherlock. What are you doing here?"
He looks down at her with kind understanding. "I used to see, but didn't observe. Well, I see you know."
Molly frowns, her fingers clutching nervously at the cup of coffee she hasn't drunk yet. "What do you mean?"
"There's nothing wrong with disliking sex. Don't let anyone try and convince you otherwise."
"I do not – dislike it," she replies in a small voice, not daring to meet his eye.
"But you don't like it either," he completes the sentence for her, and that's when she looks up at last.
"Oh," she exhales, because everything is starting to fall into place for her as well. "Is that why you never…?"
"I've always identified as an aromantic asexual, but I've come to think that 'grey romantic' might be a more accurate description."
Her brow furrows in confusion as he takes off one of his gloves and tentatively reaches for her cheek. When he leans forward to connect with her lips her eyelids flutter shut in what he's fairly sure constitutes delighted approval.
Now that sex is off the table, there's nothing coming between them anymore.