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He doesn't really know what kind of relationship Irene and Sherlock have. They seem to dance around each other, close, but never quite touching, in a way that is almost surreal to John now that he's got Mary. They seem quite content to skirt around the other, flirting and playing the game but never raising the stakes.
John can honestly say he doesn't understand it.
Why do they wait?
Both their lives are dangerous, and one of them is likely to die before the age of fifty if the rest of the world has its way. But no, no matter what John tries to hint at, and he makes hints that he knows both Irene and Sherlock understand clearly, neither of them want to tell the other how they feel, perfectly content to hide sentimental things like feeling in the darkness of the shadows.
Neither of them are willing to risk telling the truth, because with the lives they life telling the truth is a dangerous game, and not one either of them are willing to play.
And they are on a boat sailing over the English Channel, Sherlock looking more serious than John had ever seen him, with a bloodied handkerchief clutched in his hand and the stitched letter IEA barely visible in the corner.
Sherlock stands up and lets the handkerchief go, flying out over the water.
John watches it settle and then start to sink, falling beneath the surface.
Neither of them told the other how they felt.
And if Irene is gone like John suspects she is, John knows that his friend is suffering pretty badly right now.
only Sherlock is Sherlock, and even John doesn't know what to do with him, so he pretends he can't guess that Irene's dead, and pretends that death is something that doesn't happen to any of them because it's easier that way.
Death doesn't exist for them, or else Sherlock will start to regret things and then Moriarty will get away.
And that's something none of them can afford.