Okay this is a very small and overlooked thing in the story but I do think about it sometimes. So in the comic and Epilogues, there's like one or two moments where Karkat specifically mentions Nepeta after she has long since died and they haven't seen her before. The first time is when they're all on the meteor for a second time and he makes some offhanded comment about the Dreambubbles, more specifically that he's not too bothered by not going through a lot of them on their long journey through the Medium, since he's sure it would've been "great" to just hang out with a bunch of "Dead Nepeta's".
And then again he mentions Nepeta in the Epilogues when Sollux and Aradia seemingly just show up out of nowhere, saying "Who else is gonna show up, is Nepeta back somehow as well!?" (I'm paraphrasing all of this and cannot find the original screenshots of these conversations pls forgive me this is quite a long comic book)
Anyways, all this to say, Karkat always seemed to act like Nepeta's small crush on him was really annoying and weird, and sure I won't say that Nepeta had like 0 issues. But I also think maybe he feels he could've been nicer to her or something before she kicked the bucket in such an awful way you know T_T? And then he tried to "fix" the guy who murdered her and that didn't work out well at all.
Also in the beginning of Act 5 when he's asking each of his friends if they want to join the game, even though he "hates" roleplaying he still decides to play along with Nepeta's roleplaying anyways (even if he's being an incredibly abrasive sarcastic asshole the whole time T_T) I always wonder if maybe he felt a little sad that she died like that, like sure she was "annoying" but I doubt Karkat would want to wish death on the poor girl.
Well if he doesn't miss Nepeta I certainly do </3
