I mean technically Mecha Fiora was in Smash 4 as a trophy but uh... alright. Plus I mean... I'm the type of person that says if you're complaining about spoilers for something that's been out for more than five years, its on you and your fault and its essentially free game. But I see where you're coming from.
While in Japan the first game has been out for more than that and the first game has been out for almost six years now (in Japan it's been out as long as Xenoblade 1 has), I'd say Junko with Monokuma is fine, especially since in more recent DR-related things, she's not necessarily the "main antagonist", not gonna name them since they've been out for less than five years but those with knowledge know why. That said, Smash and its consistency with the lack of spoilers or giving spoilers is a messy history, doesn't help in the case of avoiding spoilers some official marketing and such though has essentially already given her away.
Just searching "danganronpa" in youtube gives you a few videos with her in the thumbnail within the first ten videos, at least for me anyways. Same somewhat goes for if you search up "danganronpa anime" as well. That said just searching up "monokuma" in youtube has her in the thumbnail of the 23rd video.
This is obviously something highly debatable and I can do with or without Junko in all truths but until for example... we get a DR trilogy on the switch, I don't think it'd be that much of an issue to include the actual Junko in, that said I do expect her to be more so a spirit than anything else.