Once again, you clearly aren't paying attention to what's being released for this platform on the Japanese and American Virtual Consoles.
Several games that haven't been in Playstation 2 collections that haven't been seen since their original retail run are being brought over by D4 for North America. Blue's Journey, Magical Drop II, Ninja Combat, Ironclad, Street Hoop, and Spin Master all jump out when I look at the list of released games as games I haven't seen on compilations.
I fail to see why Windjammers is going to be any different then these games. Clearly D4 is still supporting this as seen by several NeoGeo releases in recent weeks that made it out earlier in the year in Japan. They're releasing much more then just Metal Slug, Art of Fighting, Fatal Fury, World Heroes, and King of Fighters on this service.
I guarantee to you that Windjammers will make it out eventually. [Edit: As of April 2014, this never happened and the Japanese download was delisted last Fall. You win some, you lose some...]