Arthur Conan Doyle knew there was an issue with Watson's sexuality and his relationship to Holmes. He didn't handle it very well as it turned out. He lamely tried to have Watson dropping his practice and wife at a telegram from Holmes. But what doesn't work well in a short story works even less well in a long-running television series. Has nothing to do with sexism. Is there some determination to misunderstand even the simplest thing?
There is no issue in any single episode of Elementary. It's a question of how they will handle it if the series is successful. If they give their Holmes a sex life it will be a risky break with tradition. If they give their Watson a sex life, it will mean writing a sex life for a woman lead who can't be thrown into the refrigerator. Yet given the premise, the woman in this case can't be defined by her sexuality.
And it's not a question of flirting with Holmes. This Watson is supposed to already have a life of her own, and unlike this Holmes, hasn't left it thousands of miles away. Has she no one to go to the opera with?