I think porky and sylux are the big characters to look at that dont have spirits because of various things about them.
third party characters not so much as nintendo not including them as a spirit MIGHT be something negotiation-wise we really cant say, where as first party nintendo characters being absent is entirely on nintendo... so missing third parties probly dont mean much save for maybe heihachi since he was a mii costume and considered for playable before and now has nothing. feels like a good spirit candidate and namco working directly on smash makes them the loosest company to get stuff from but hes gone.
porky being such a big part of SMASH in the past makes his absences the most suspicious imo, not only a history with the mother series and important to both ness and lucas and a stage in smash but he's always been well repped in smash and now is gone completely from what we've seen and isnt even referenced for his status as a former boss fight... HIGHLY suspicious i'd say. Also while its seen as almost an impossibility at this point, localizing mother 3 and promoting that with a smash character would make sense with nintendo choosing the dlc.
sylux, while some of the other hunters are gone, was always a fairly likely dlc candidate with nintendo picking the chaarcters and metroid prime 4 being a BIG future title to promote and sylux supposedly having a major role in there... just adds even more to the chances of being DLC to have sylux missing from the spirits.
no idea if spirits "deconfirm" characters or what i think theres decent arguments on both sides but i still think in case it DOES deconfirm its worth looking at the characters who managed to avoid being spirits. with potentially only 5 dlc characters (6 with piranha plant and yes 30 potential spots have been found but lets stick with what we know for sure) and some likely being third party a missing major nintendo character or two when almost everyone else is a spirit is enough to possibly narrow down a dlc character or two. and if you dont think nintendo would be that obvious in giving away the dlc characters... let me introduce you to box theory.