Lalo almost certainly has to be dead. When Gus kills Don Eladio and his family, he goes back to Hector and says all of them are dead and the Salamanca name dies with Hector. Lalo has been a big figure and disruptor. If he's still around in Breaking Bad, I couldn't imagine he would only get one passing mention. Gus wasn't introduced in Breaking Bad until season three so Lalo could still very much be alive in the beginning of Breaking Bad. It would seem obvious that Mike and/or Gus kills Lalo but I have a feeling it will be something unexpected like Lalo killing Howard.
I'm also reminded that Skinny P set the meeting up between Tuco and Jesse since he met Tuco while in prison. Tuco is currently in jail so we may have a Skinny P sighting. The scene where Walt bombs Tuco's hideout is where we may first be introduced to Walt and Jesse.