They have, I think. In my current DW game, I (Minamoto -> Japan) was the one to annex Ryukyu, and that was after I formed Japan, so they survived on their own until the 16th century just fine; in that game, Ming blobbed all the way to the Caspian Sea but didn't take Ryukyu. My other save games (Sweden 1446 and Hindustan 1550) show a pattern of Ryukyu surviving at least 50 years.