When Irene Adler got involved, John got angry.
He didn't mean to, he certainly didn't want to and he didn't want it to happen again, but it happened.
He wasn't angry at first, of course, not really. At first he simply had no idea where to look.
No, at first she was simply, what Sherlock would call, interesting. Dangerous, yes, of course, but in an easy, manageable way. A way which meant you might lose your liver, your dignity and possibly your wallet.
Then she got dangerous in a less manageable way. She got dangerous because she started playing certain games with a certain consulting detective and, for once in his life, Sherlock played back.
He pretended he didn't, he pretended very well. If John didn't pay attention to every little thing that Sherlock does (not-that-he-does) he might not have noticed. He pretends he hasn't, Sherlock would prefer that. And John Watson does what Sherlock Holmes prefers. Every damn time.
Of course then Irene Adler dies, and Sherlock stops bothering to pretend he doesn't care. And John has no idea what to do and that hurts...
When Irene Adler decides she isn't dead John gets furious.
He didn't mean to but he certainly doesn't mind this time. This woman hurt Sherlock. For months he's been grieving, pining and absolutely insufferable.
John thinks that this woman should suffer through an insufferable Sherlock too, share some of that around. Til he realises that would mean that she'd have to get near Sherlock for any length of time in order to suffer through him... John changes his mind.
John doesn't get angry when Mycroft tells him that Irene Adler is actually dead this time. He doesn't get anything much. At first he feels slightly worried - worried for Sherlock. Later, after he tells Sherlock he'll never see her again, he just feels hollow. He wonders why for a while but then he decides he might not like the answer, so he stops wondering for a while.
It's only when he's staring at Sherlock one day that he thinks he might know.
Sherlock didn't react. He didn't react at all to the fact that he'll never see Adler again.
It makes John wonder if that's what Sherlock will do if he ever leaves him.
It crosses his mind to ask the detective, he wonders what Sherlock would say... but then he decides he might not like the answer, so he stops wondering for a while.