Dumbledore knew about the Vanishing Cabinet, but may not have known where its twin was or if it even existed, as the cabinet didn’t work too well after Peeves dropped it. The Weasley twins stuffed Graham Montague in the the damaged cabinet and he was sometime later found having Apparated into a toilet, even though he didn’t have an Apparation license and (*PLOTHOLE*) humans can’t Apparate in the castle except during the Apparation lessons. Montague ended up such a mess that he was disoriented for weeks, and his parents showed up at the school because of it. However, he did tell Draco that he could hear going ons inside Borgin and Burkes, but we don’t know when he told him.
I think it likely that Umbridge had the house-elves put the cabinet with all the castle’s other surplus items and broken furniture, not caring where, just “get it out of here,” so it went into the Room of Requirement. After all, Umbridge didn’t want anyone else to stuff another student into the cabinet—I’m sure that Mr. and Mrs. Montague told her off and warned her what would happen if it ever happened to their son again.
The next year, Dumbledore may not have noticed when he collected the store keeper’s memory of Tom Riddle that other cabinet was in the store. One may have been painted a different color, or maybe they didn’t look identical. He had other things on his mind than why Draco’s body guards were Polyjuiced into first year girls, standing around in the castle’s hallways— knowing where Draco was and what he was doing at all times was Snape’s job.