As mentioned there are 3 ways for this to be true:
1. He never ate the Nika fruit (low possibility) or it was his powers rather than a DF, which later gave rise to the fruit.
2. He officially died but was resurrected in some way (hence his body looks so weird and he's clothed). We've seen lots of cyborgs - there's a lot of mystery
3. Someone with the Yami Yami fruit removed it from him
or bonus 4. Since we've seen evidence of the nika fruit possessing its own will (avoiding the gorosei for 800 years) - it somehow spontaneously left him.
We don't actually have yet a history of when fruits were created but I think there are fair reasons I've stated why "Imu-boy" would not possess the powers now (and why he wants it back).
And we still don't have a true history of that fight so to say Imu was involved against Joyboy is also speculative. We know they fought the 20 kingdoms and the 20 kingdoms didn't know how the world really works.
Oda can do whatever he wants of course. I'll just respond based on what we know so far...
1. Joyboy and Nika aren't the same person. Nika should have been a legend in that era. (Maybe the ancient Giant Kingdom had slaves who believed in Nika? Joyboy could have been an escapee.) If you want, you could speculate that Joyboy's wish created the devil fruit. We don't know how the wish thing works, though.
2. Maybe someone with Brook's fruit can awaken and use it on someone else?
3. Every case we know of with devil fruits being stolen involves somebody dying. I suppose you could loop that around with #1 and make it so pirate Joyboy had the fruit stolen and then was resurrected but wasn't himself anymore became corrupted, along with the duplicate Nika fruit.
Other folks have come up with other ways for Imu to have similar reality-bending powers that I think are more satisfying though. I forget who it was, but someone suggested that since Oda apparently said once it was difficult having a Jerry-like character without a Tom, maybe Imu could be more of a Tom equivalent.
I know what Ivankov said isn't technically confirmed, but it would be a very bizarre time to introduce false info. At the least, what he said about the historical Nerona Imu should be true and we can doubt for now if the Imu who sits on the Empty Throne is the same person.