I assume she's still alive, yes. It just seems like an oversight; her getting shot is basically a throwaway line by Murphy that isn't brought up again. I know Dresden's priorities are different in the last three books, but it feels out of place for it to be totally unacknowledged.
I mean, in Turn Coat, Will and Georgia are with Andi the whole time they're off-page, and this was after Kirby was killed; sure, they're a pack, but I'd expect someone to be with Abby, you know? Especially because Toto loves Will. But everyone we see at the Chicago Justice League Meeting at Murphy's house is running around with Dresden. Heck, Murphy's hanging out at the BFS when we see her next. Especially odd given the attacks that were going on throughout Chicago at the time; she's in a hospital, and vulnerable.
Am I reading too much into it? Yes. I am. I'm nitpicking. I plead guilty.
But damn it, I love dogs and dog owners. I want to know that Abby and Toto are okay, because I'm emotionally invested in their codependent relationship.