Karkat very much (at least to me) seems like the type of guy who's really compassionate and caring but is just hesitant to show it or get too personal, hence why he's always so angry, but in a way that doesn't feel like he's genuinely enraged at absolutely everything all the time and more just seems generally irritable. Even though he digs at them a lot, he always seemed to want the best for his friends and tried to do what he could that would, in his mind at least, give everyone the best chance of success, so I can imagine he probably does miss Nepeta since I remember in one of the Openbound (I think?) sections he tells the ghost version of Aradia something along the lines of "Y'know, if I could go back in time and stop you from dying, I would right away", which in the moment seems like him just being annoyed by her vagueness and mystique, but if you look a bit into it feels a lot more like some genuine care shining through in the form of a slightly snarky remark