Hank would certainly have a case that Walter White was the "Heisenburg" cook as Walter had the motive (he needed lots of cash fast), means(Access to chemicals, strong chemistry knowledge, and connections to distribution networks) and opportunity (Walter had time to do the steps required of the operation).
Notably, the money doesn't need to be there to show evidence of the crime (Possession with Intent to Sell being the driving one). Hank was, from early in the series, well aware of a list of crimes attributable to "Heisenberg," but didn't have a person to charge with these crimes. What blows Walter's cover to Hank was the book of poetry Leaves of the Grass by Walt Whitman. The Handwritten dedication inside the cover is "To my other favorite W.W. It's an honour working with you. Fondly, G.B." written by Gale, who's death had previously led to a raid on the Meth Lab where Walter White and Gale had worked together and was no known to have been run by Gus Fringe (also deceased). Other evidence in Gale's office were notes regarding the cook operation at the Fringe Lab, with the quotes attributed to then unknown to Hank, "W.W." and his own notes attributed to him as "G.B." (I believe Gale did have Whitman books in his home).
Walter had previously told Hank he had no idea who Gale was, so seeing a book that Gale personally dedicated to Walter and attributing him as the other favorite W.W. would be as easy as comparing handwriting samples from Gale's notes to the snippet from the book, thus linking Walter White to the Heisenberg ring. Hank also discusses that he believes Gale is not Heisenberg as Gale was taking extensive notes from another source in meth production and did not have any ties to the known distribution chain outside of Gus Fringe.
What complicated Hank's ability to prosecute was that Marie (aka Jesus Christ-Marie) had knowingly accepted dirty money from Hank and Skylar, believing it was from illegal high stakes poker and not drug money... but reporting Walt's source of income meant implicating them in the crime, which Walter and Skylar use as blackmail against them by creating a confession tape that would implicate Hank as the Mastermind of the operation who forced them to perform their illegal actions. This would have cost Hank his career and would have netted the Whites a not guilty plea as too much doubt would have existed to convict (The Schraders would not be convicted by the same reasoning, but Hank was the primary breadwinner and out of a job... and likely not hireable by other LEO organizations as the controversy of the matter would make him untrustworthy to have on, and the inability to realize a close family member was a drug lord made him look incompetent. I call this last part "The Spycatcher's Dilemma" as if there is no evidence of a Spy, the spy catcher is criticized for not finding spies. When a spy is caught, the spy catcher is criticized for not catching the spy sooner.).