This information was revealed literally months after the Virtual Console was first released in 2006, not sure why some people are so surprised Nintendo handles all the games for their systems, Sega handled the Sega systems, Hudson (RIP) the TurboGraphix and SNK the Neo Geo.
Of Natsume isn't exactly innocent in this. If Capcom was able to get something as obscure as Demons Crest released last Summer, Natsume sure as hell could have gotten more of their games released as well. Seriously, this is like how SNK said Metal Slug Anothogly for the Wii released shortly after launch didn't have Classic Controller support because they said Nintendo told them all retail games needed to show of Wiimote control and the CC was only for Virtual Console games. Of course this was 100% made up bullshit which was a proven lie since a DBZ fighting game released around the same time allowed it. Or like how Sega said the reason Sonic CD wasn't in Sonic Mega Collection for the Gamecube was because the lack of data on the disc, because we all know a dozen Genesis games easily fill up 1.5 GB.
This is your typical third party finding a way to blame their own lazyness on Nintendo. Yes Nintendo has done a bunch of stupid **** with it, but as I said before, if Capcom could get Demons Crest released then Natsume sure as hell could have gotten Lufia 2 which is a lot more famous on the Virtual Console if they really wanted too.