Incidentally, it's the same reason why Ayumu Tachibana *sob* and Takamaru *sniff* were rejected in Melee and Smash 4 respectively: they're not very popular outside of Japan, if they're recognised at all.
Little Mac can be considered an exception to an extent, since his game was designed by a Japanese-American team and Punch-Out!! had the most success in the US, but he's still an iconic character from Nintendo's early years, he was an Assist Trophy in Brawl and Punch-Out!! Wii had a very successful worldwide release. Some Japanese fans may not have recognised him initially, but he didn't have quite the same "Wait, who?" reaction that Marth did and Ayumi would have had.
Which is why I think Shovel Knight is a peculiar case. I think that, if he does get in, it will be due to Nintendo deciding it'd be a good business venture and convincing Sakurai that it's a good idea. Short of Sakurai being a big Yacht Club fan, I can't see him voluntarily adding the character over others.
Which is why I think the "third-parties have a better chance than others" theory is tish-tosh. DLC is going to factor in Nintendo's executive opinion, that is certain, but I don't think Sakurai will just say, "Yeah, this obscure character that has no direct connection to Nintendo is doing pretty well, I'm gonna go out of my way to negotiate the rights with the creators despite being on a tight schedule and having a relatively tiny dev team."
I'm being facetious, but you get the point.
Point is, I can only see Sakurai go in for Layton or Jibanyan (nothing against either character, before fingers get pointed) if Nintendo cajoles him into doing so for marketing reasons. Otherwise, with the rich canon of first-party characters at his disposal (most of whom, let's be honest, have waaaay more support than the vast majority of third-party characters whose name isn't Snake), I don't see why he wouldn't just satisfy the fans directly with the characters that have been more consistently requested and who don't require complex investment contracts to get in.