I mentioned it briefly in an art post on here, but I do not believe I have gone into detail about my personal headcanon for Jon's place on the Asexuality spectrum and how that presents in the version of Jon that I draw.
My Jon IS asexual, as in, he has a very low libido and does not actively seek out sexual encounters. His actual aversion to sex, however, has more to do with crippling sensory issues when it comes to sweat, saliva, and other bodily fluids. The sensory experience that is pretty unavoidable with traditional (especially penetrative) sex, is wildly unappealing to my Jon.
This is not to say that he does not enjoy physical -- or even skin on skin -- contact. I personally believe that Jon is tragically touch-starved from a life without caring individuals in it. He did not have parents throughout his childhood and his grandmother certainly does not read as the affectionate type, and when he finally did become an (albeit stunted) adult, I imagine him quickly realizing that he did not want the form of intimacy that his peers had to offer him, and could not articulate what he DID want, so he resolved to dismiss all of it entirely.
Best not to let people in on any more ways that he is 'complicated'. Better to say 'no' outright than to list all of his weird stipulations, just to be turned down anyway.
Elias Bouchard is the turning point.
Jon gets from Elias something that he has never received from anyone else, and that is complete understanding without judgement or pressure. Jon doesn't need to dance around his specificities and preferences with Elias, because Elias always gets it right the first time.
In pre canon and the first season, I picture this resulting in Jon experiencing an almost-unwilling sense of comfort in Elias' presence, then, eventually, the beginnings of an embarrassing crush on his employer. Jon is not afraid of Elias, because even when he oversteps, it somehow always manages to be in a way that avoids Jon's triggers; Straightening Jon's tie for him, but making sure not to touch his throat, taking his hand to guide him places, but never pulling his chair out for him, because Jon has a specific way that he does that to avoid making any scraping sounds, etc...
Later on, after Jon becomes Archivist and Elias' abilities come to light, Jon feels stupid for not realizing the GLARING coincidence that all of Elias' perfect behavior added up to be. He is irritated and feels lied to. Yet, a small part of him is well aware of the fact that Elias' skill set makes him uniquely equipped to handle Jon in a way that Jon would never know how to facilitate in a relationship with a regular person.
When their relationship DOES begin to turn intimate, it is out of Jon's need for guidance and submission. Elias is the only person on Earth who already knows Jon's boundaries, and even knows them better than Jon himself. It makes it so easy for Jon to let his likes and dislikes be coaxed out of him, because they are already open secrets.
Elias is the first person to ever hear Jon admit that he likes sexual intimacy, but only when it is performed clothed. He prefers aimless foreplay for its own sake opposed to seeking release, and in fact, the release is not a required aspect at all, just something that sometimes happens as a result of the parts that he actually enjoys. He appreciates skin to skin contact, but only when sex is not involved, simply being held platonically and without expectation.
Elias is exactly what Jon needs to admit these (in his perception) shameful things. Patiently prompting "very good, and what else?" When Jon's confidence begins to falter. Always knowing when he needs encouragement.
Elias Knows Jon in a way that no other living thing, save for the Eye itself, is capable of Knowing him -- And he loves him 'FOR' all of the things that make him odd and occasionally off-putting, not in spite of them, since Elias' favorite form of intimacy is laying bare the very soul of a person, however rotten that soul may be, and seeing ALL of them as they truly are.
Jon is very appealing to Elias inherently, because he happens to be both a terrible liar and a closed book. Jon will not ask for the things that he wants and needs, he will not share anything that isn't forced out of him, he will never explain WHY something bothers him, he loathes his own personality and attempts to mask it by mirroring figures of authority... Elias' nature overrides all of Jon's walls and he Knows Jon regardless of his rigid unwillingness to be known. Jon hides and Elias Sees him anyway.
-Which just so happens to be the only way to make Jon accept accommodation. Through the resignation that comes with certainty that Elias 'already Knows, so what is denial but a waste of energy and breath?'.
They are not, by any means, healthy, but they ARE a perfect fit. A beautiful, horrible feedback loop of Beholding and being Beheld.