It's a misconception that most of the artworks hidden or stolen during WW2 are truly 'lost'. It's certainly the case that many paintings, sculptures, rare books and antiques were 'expropriated' (looted) by the Nazis, on a small scale from individual Jewish families, and on a large scale from the museum collections of occupied countries. However, the process of expropriation was usually well-documented, and the locations of looted works were, more often than not, easily traced.
The Art Loss Register, the international body which maintains a list of all stolen and missing artworks, estimates that about 200,000 works were stolen during WW2, but of those, around 170,000 have been recovered, with 30,000 still missing. Today, reputable museums will consult the register before acquiring something for their collection, if there is even a possibility that the piece might have been looted during WW2. (Source: me, I'm a curator).
Perhaps unsurprisingly, those works which are still missing tend to be the ones which were stolen from private collectors, or art dealers; such as Raphael's Portrait of a Young Man, stolen from a Polish family, and a Klimt portrait originally in the possession of a Viennese Jewish collector. That said, most 'lost' works are lost only in the sense that they are no longer with their original owners, or the owners' descendants - the actual locations of the works are frequently common knowledge, as was the case with several pieces in the possession of Horst Wächter, the son of Otto von Wächter, Nazi governor of occupied Poland. Similarly, Klimt's famous 'golden' portrait of Adele Bloch-Bauer, which was expropriated from her family after the Anschluss, was openly displayed at the Belvedere Museum in Vienna for decades, until Bloch-Bauer's surviving niece successfully mounted a legal challenge to have it returned to the family.
Large museums had - and still have - systems in place for controlling their inventory, its condition and location. For example, during the German occupation of Paris, the Jeu du Paume courts near the Louvre were used as a kind of depot or staging post for looted artworks from French museums and private collections. Ostensibly working under the orders of the Einsatzstab Reichsleiter Rosenberg, or ERR, the Nazi taskforce established to oversee the expropriation of cultural treasures, the French curator and art historian Rose Valland was responsible for taking an inventory of all the artworks which passed through the Jeu de Paume. Unknown to the ERR, Valland (a) spoke excellent German, and (b) was an agent of the Resistance. She made secret copies of the inventories, which would subsequently allow most of the works which passed through her hands to be recovered after the war. Furthermore, she passed information on to her Resistance contacts relating to the shipment of artworks by rail, so that they would not mistakenly be blown up during sabotage operations.
That said, there are - as OP asked - definitely still hidden caches of looted art to be discovered. It is highly likely that many missing paintings are locked away in Swiss bank vaults, which is thought to be the fate of the Raphael portrait mentioned above. In 2012, a collection of over 1400 artworks was uncovered in the Munich apartment of Cornelius Gurlitt, a collector and art historian who was being investigated on tax evasion charges. Gurlitt was the son and grandson of notable art historians, and his father, Hildebrand Gurlitt, had collaborated with the Nazis on the expropriation and movement of 'degenerate' modern art, much of which he appears to have 'purchased' for himself at a fraction of the works' real value. Thanks to his part-Jewish ancestry, the elder Gurlitt was not prosecuted after the fall of the Reich, and claimed that his art collection had been destroyed during a bombing raid... which was taken at face value, until it showed up in his son's apartment, almost 70 years later. It is possible that we may see another 'Gurlitt' in our lifetimes, although as the period moves out of living memory, art historians will be increasingly reliant on archival records, and luck, to make these discoveries.
If I may add a follow up question, how many items like the Amber Room from St Petersburg’s Catherine Palace do we know are still missing and how does something as big as that get lost?
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