I didn't notice any joke. She replied like her dating schedule had been booked years in advance - while in reality she's meant to be isolated and deprived of any deep relationships. If you're walking down the street and suddenly, I don't know, Margot Robbie jumps out of a limo and tells you "you're beautiful" you would hardly reply with "I know" even jokingly.
Anska covered this one already really, but I'll add to it.
She was teasing you. You gave her a lame compliment, expecting her to swoon and she gave and unexpected answer. It shows that she is mischievous and playful.
It's playful and part of her character, as well as it being give and take with her when it comes to teasing. If you give her the Night Orchid, she pretends that it's poisonous and then laughs and gives you finger guns like a total goof as she says she's joking. Then when she says she doesn't have anything to give in return, you can joke that you'll just take the flower back then and she'll tease and say she doesn't want to spoil the kind gesture by breaking your fingers. She's not saying she's actually going to try and break your fingers, you're just having a laugh together and being in the moment appreciating each other. It's a moment of levity and a breath of fresh air amidst the dampened mood the shadow-cursed lands bring. If any of this comes across as her being an "insufferable bitch", trigger a "vomit reflex" or make you consider her a "piece of shit", then I believe you're seriously missing some important social cues when it comes to non-straightforward communication.
I'm honestly baffled that the "I know" line can be taken as seriously as you have and that your response is so strong to it. In all the playthroughs I've seen, as well as threads I've read discussing her romance path, I've never seen a negative response of this magnitude before.
why are all three main male companions so pleasant to interact with, while two out of three female companions come across as insufferable bitches
I'm very surprised that you have such a strong negative response to Shadowheart's joking "I know" line, to then in the same post say that you find Astarion so pleasant to interact with. Astarion is also jesting about it most of the time, but he has so many "I know" lines in his dialogue in both the platonic and romantic paths. And the first part of his romance path isn't even sincere, he'll give (mostly) fake compliments to lure you in and then use having sex and feigned romance with you as a means to have you become protective of him so that he can feel safer. He only starts feeling more for you later on, but right up until rejecting the ascension, he's probably the most selfish companion only ever acting out of self-interest. And if he does ascend, he wants you as a thrall rather than an equal, continuing the self-interest and taking it to the next level on a path to become the new Cazador. DJ Shart has the decency to straight up tell you that on the path she's on she can't allow actual love into her life and that she thinks you do deserve to find it if that's what you want. So on that route she communicates clearly and gives agency to you to find happiness beyond her if that's what you desire at that point, or choose to stay in a pseudo-relationship dictated by Shar's terms.
I love both Astarion and Shadowheart as companions, I find both their routes intriguing and statistics show they're also by far the most chosen romance options. I'm just confused how you end up classifying one as an insufferable bitch and the other as pleasant to interact with. I've noticed a lot of talk about the differences between male and female in previous posts as well, as well as just now saying you gender-swap mod Shadowheart and Lae'zel so that killing them doesn't interfere with your male neurons, so I was wondering something. Could it be that instead of the actual character writing, it's instead because in the base game you find it less offensive if a male Astarion has an "I know" line and much more offensive if a female Shadowheart has such a line, perhaps?