I think she’s deliberately adversarial toward Sherlock so he doesn’t look deeper into her false male persona. He probably dismisses her as a one of those short men who feels he has to prove himself (Napoleon complex sort of thing).
She looks amazing as a dude.
Her moustache is clearly superior to John’s.
She’s a BAMF
She got to be the Bride that scared the bejeezus out of Watson and probably loved every second of it after he let her know he knew she was actually a woman!
“Hooper.” “Holmes.” He still calls her “Hooper” without adding any sort of condescending “Miss” to it when he greets her in the desanctified church. And he instantly knows who she is when she speaks. Does that mean he knew she was a woman all along? Jury’s still out on that for me.
Oh, and, the biggest two cents’ worth of all: she’s NOT some sort of symbol or stand-in for John. Just like the picture of Irene in Sherlock’s watch is not some sort of symbol or stand-in for John.