There’s some ambiguity on this point. I’m pretty convinced that John was enamored with— maybe even in love with— Sholto. The question is how far it went.
I have several friends on here who are 100% convinced that jolto is canon. I think it definitely could be, but I’m not sure if we can assume that it was. Basically, the way that John looked at Sholto at the wedding (and Sherlock’s jealousy, which is even worse than when John is with Mary) convinced me that there’s more backstory than they are letting on.
The thing is, the way John acts with Sholto is not that different than the way that he acts with Sherlock. I’m not doubting that John loved Sholto and that he may have had sexual/romantic feelings for him. The question is whether they ever ACTED on it. In that way it’s very similar to johnlock— to me, it’s “canon” in terms of the intent (they obviously love each other), but it hasn’t been “consummated” (which is an extremely awkward word, but the only one that can really be used for this).
In my headcanons, John and James at least kissed and/or had a few encounters when they were abroad. Whether we will ever actually get confirmation of it on the show is another thing, but by god, I would LOVE for that to happen. Why? Because we would have canon confirmation that John is a bisexual character. That would be beyond fantastic.
The line “we weren’t the first” has definite sexual connotations to me.
And the thing that people forget is that the little beaming man in the freeze-frame is John “Three Continents” Watson.
He is clearly officially taken when he’s with Sherlock (“Three Continents is sleeping on the COUCH?”) for what are, to me, obvious reasons (*AHEM LOVE SHERLOCK AHEM*), but it may be assumed that the captain is a sex god.
Sex god + not the first + adoring glances + Sholto with “we are the same, you and I” to Sherlock + so many other things with lighting, innuendo. Etc = Sholto is an ex held in high regard.