While trademark renewals are nothing new and generally don't tend to mean much beyond a company ensuring the name of its IP isn't used for another product, this is slightly different in that it's an entirely new filing, as opposed to a renewal.
Nintendo already holds trademarks for the game's Japanese name, Wish Room, as well the Japanese name of its sequel, Last Window: Mayonaka no Yakusoku (Midnight Promise), but this appears to be the first time its Western name has been trademarked in Japan. Hotel Dusk: Room 2015, which was developed by the now-defunct Cing, was released on Nintendo DS in 2007 and gained a cult following for its unique art style and its pulp novel storyline which extended to having to hold the DS vertically like an opened book.
Its sequel, Last Window: The Secret of Cape West, was released in 2010 and was the last game released by Cing before it went bankrupt two months later. The reason Hotel Dusk's trademark filing has raised eyebrows is because last year Nintendo released remakes of two other cult favourite Cing games.