I feel like it's almost confirmed that Joyboy and Nika are separate characters.
Vegapunk mentioned Joyboy in his message to the world in Chapter 1114, but never said anything about Nika.
The Giants all talk about worshiping the Sun God Nika but never mention anything about Joyboy.
Most of the time, the two characters aren't mentioned at the same time. It feels almost certain that they're two different characters that existed at two different times. Nika in the First World and Joyboy in the Second World/Void Century is the most likely scenario. I'd be VERY surprised if they turned out to be the same exact character at this point.
First of all, NONE of the mythical fruit beings are real, are they?
Well...actually...
Kaido's Devil Fruit is a "mythical" Dragon Fruit.
https://onepiece.fandom.com/wiki/Uo_Uo_no_Mi,_Model:_Seiryu
And we know that some form of dragons existed in the One Piece World, long ago. Ryuma killed one in his "Monsters" one shot, which is canon to the main story. This was a LONG time before Vegapunk's experiments. So, there were naturally occuring dragons out in the wild on this world at one point.
https://onepiece.fandom.com/wiki/Shimotsuki_Ryuma
(There's also the Sennenryu or "Millennium Dragons" that we saw during the Warship Island Arc. And, sure, that's a anime-exclusive filler arc. But, it's technically the first appearance of a form of the Voice of All Things, and it was originally considered to be a possible movie plot. Personally, I think Oda might have had a bigger hand in this arc's plot than we originally suspected. It may or may not "count", depending on how you feel about these things. But, it's something to keep in mind.)
https://onepiece.fandom.com/wiki/Ryu
https://onepiece.fandom.com/wiki/Warship_Island_Arc
So, if dragons existed at one point, that means Kaido's Devil Fruit isn't based on something that's 100% fake. Which means the "Mythical" designation doesn't mean those creatures didn't exist. It's more "Mythical" like being rare and powerful. Possibly "Super Ancient" or some such. Existing so long ago that no one even remembers them existing.
But, it kind of depends on where Oda goes with this. The various "Mythical" Fruits COULD be based on things that actually existed in the past. Or it's possible they come from other planets, bringing more science fiction elements into this. Or it's possible that Oda could make it so that the Devil Fruits themselves made these creatures exist in real life. Kind of like how Aokiji and Akainu's battle on Punk Hazard changed it's environment, it's possible some of these Mythical Devil Fruits "Fully Awakened" and transformed the local wildlife to mimic animals that were only stories beforehand. The Devil Fruits could have turned fiction into reality.
But, there's one thing to keep in mind. Oda seems to have a ongoing theme that everything that's considered "fiction" in this World has some basis in reality. Not every story we hear is 100% true...but no story seems to be 100% false, either. The Mermaids, Germa 66, the Dragons, and even the One Piece were all considered to be things that were just made up fairy tales. Things no "reasonable adult" should believe. But, all of them have proven to have some basis in this world's reality. Every "lie" contains a grain of truth. Even Usopp's lies tend to become the truth, if given enough time.
So, personally, I feel it's pretty likely that some form of Nika existed. Maybe not as we think of him. And Nika...may not turn out to be "human". But, I think Nika will turn out to be something that existed. And probably had some form of mind and will of it's own. "Nika" might turn out to be a mass of sentient "Dream Energy" given form by humanity's wishes. But, as we've been told, the Nika Fruit seems to have some form of will of it's own. It seemed to be running away from the World Government. And that's probably going to turn out to be the literal truth.
I don't think the myth of Nika will turn out to be a total lie. It may not be the total historical truth. But, I think there's going to be a grain of truth in it. Nika likely existed. Nika likely still exists. And Nika may be pulling strings behind the scenes of the story as we speak, through Luffy. Time will tell.