I'm not sure if there's any place left in Indonesia that still bear the name of a Dutch queen/king/prince/princess/etc. But interesting! I shall find out.
I know in Southeast Asia, the Philippines is named after Philip II of Spain....
There's a "sort of royal" Prince Wiraguna who lent his name to the area "Ragunan" (meaning the place of Wiraguna) in the South of Jakarta.
Actually he's a rich landowner of Dutch-descent, his name was Hendrik Cardeel. For services to a local Sultan (saved the Sultan's life, basically), he was given a royal rank and a royal name "Wiraguna". Prior to that, he was already given a rank of honor as the court architect.
Another area, Kemayoran (land of the Major) was named after a not-so-royal but very rich landowner, a Chevalier who arrived in Jakarta (then Batavia) during the Franco-Dutch war. His name was Isaac de l'Ostal de St. Martin, and held the rank of Major and sat in the Council of India. In addition to his deep interest in botany, he's also a shrewd tactician, politician, and soldier. His lands (now Kemayoran, an administrative district in Central Jakarta) were gained through various gifts from various parties he helped (yes, devide et impera rules the waves
Also, the capital city Jakarta, was named after the Prince Jayakarta/Prince Jayawikarta, who held the city after an inter-kingdom war prior to the arrival of the Dutch. When the Dutch arrived, they seized Jakarta and renamed it Batavia after a Dutch city. After the independence the city gained back its name.