This is the biggest plot hole in the show. Hank would have absolutely connected the license plate with the previous bust that Walt did his ride along. I think this is why Hank never mentions the plates, but strictly uses make and model. I think the writer's knew to keep it out of the audience's mind by not having Hank ever say the LP.
It doesn't matter that Emilio was arrested and presumed to be Captain Cook. More connections emerge. Crazy 8 snitched on Emilio, and both of them went missing. So that's a huge flag. They show Hank looking at an evidence board where he also connects Tuco to the two missing meth dealers. He utters something like he knows the connection is right in front of him but cant see it.
Jessie's car is with Tuco, and for that Hank brings Jessie to the station but can't get to the bottom of it; especially when Salamanca doesn't snitch. Before we discuss why Hank should also connect Walt, let's first get to Hank's bad policing.
Hank suspects Jessie of dealing with meth. Where did the $60k in the red duffle bag come from? Jessie denies that it is his. Fine. So why doesn't Hank utilize Walt? He could say something like he knows Walter reconnected with Jessie to buy weed. Hank could then try to bleed Walt of any info regarding meth. Like "has Jessie ever offered it to you, or have you seen any meth with Jessie?" Hank is clearly frustrated that Jessie walked, but Hank doesn't bother to question Walt. The school science lab theft is also on his mind. Why not assume Jessie, a former student, is the culprit? Again, another reason to talk to Walt.
Of course there's the security footage of two idiots stealing methlamine. Hank knows the new cooks are a duo. Jessie and Walt are slapping him in the face. Walt goes missing exactly when Jessie goes missing (when Tuco) has them. Walt is science smart but has no street smarts. (Hank's reaction to security footage) He directly knows Jessie (theCAPN) is clearly now mixed up with meth. Even if Walt is an unthinkable suspect, good police work would still be open to it, especially with some many clear connections and amazing coincidences.
If you rewatch 2nd season, it is clear as day. Hank is a good cop. He wouldn't have missed it. Especially with Walt acting weird with Hank (like why do criminals become criminals).
It is a genuine plot hole.