I think the books are a way to tie off the loose ends in veronica's story and set her up for the revival (or the rest of her life?). TDTL answers the question 'did Veronica want to see her mother again? Does she miss the mothering she didn't get? " and the answer is 'no'. Then, because Veronica wants to know her half brother, Veronica is stuck with having to develop a relationship with her mother. So there are potential storylines there. Veronica and Keith are working together as separate but equal partners and don't know much about each other's business. So Keith has let go of micromanaging her. Still he doesn't want her to know the things he is doing and there is a huge storyline there, where she stumbles into his work by accident and the two of them work together. I wonder if this doesn't happen in the revival?
I don't think Logan really gets an arc, though. I think he got a paragraph of backstory, written before the movie, which allows his many many fans to think he has won at life and yet leaves him with no continuing storylines of his own. All of his loose ends tied off, off stage. He isn't completely a cardboard standee. We do see his hesitancy with Veronica, his nervousness about commitment. He has also clearly learned to stop before he says something he may regret. In season 3 he breaks up with 'veronica because she doesn't pick up a phone call, in MKAT he runs to deployment because she doesn't come to the funeral on the first day. He runs, both times but handles the situation differently, so he still has things to fix about himself and things to learn about relationships. He is not perfect but we see how he is going to handle things. No tension, not a lot of storyline.
When he suggests to 'veronica that they get a puppy I thought more of the alcoholic's anonymous thing where you get a pet to see if you can handle a relationship with a human. Or people in general getting a pet to see if they can handle kids. I also thought that Veronica needs someone to drag her out of her work into her real life, so this is a big step for him, paying enough attention to her (and not to her reactions to him) to do something like this. His discomfort with the puppy show me he hasn't been around children or puppies much, which actually tells me he hasn't been around his co workers at the Navy much, since they seem to be family people. Hmmm. More ways he isn't perfect. But not just, or even mostly, the fear of being like his dad.
In short, they won't kill him because it will cost them viewers, since he is the main draw for a lot of people, but they have gone to some effort to make sure he remains in the background in a fairly limited role (Veronica's love interest).If they killing him would mean the revival would be about him. You'd have to see Veronica's reactions, there would be a funeral--way too much. I suspect he will show up in the first two episodes, spend a lot of time naked, he'll have a friendly relationship with Keith or/and Wallace, maybe he'll have a birthday or a promotion. Maybe even the possibility of a job that will allow him to stay with Veronica, but that will be a real change of career paths. Then he'll go on a training mission and come back at the end of the show for a couple of episodes.
If I had to bet they will be married. Mac may have joined the fbi, since she won't be in the show. Veronica will be thinking about joining her there, since she is closing in on the cut off age for special agents. Keith will be thinking about retiring. One or the other may be positioned to run for Mayor. So I suspect the angst will be from the Mars position.