Pehaps it's something like:
1- In the deep past: The Legend of Nika start (Pehaps among a specific race like thr Lunarians), the belief of this people in this entity make the fruit "manifest"
2 - Void Century: The worship of Nika is at it's peak, Joy Boy eat the Nika fruit, after this the WG work to supress anything related to Nika
3 - Presen: Luffy eat the Nika fruit
That would be the three times, because for Joy Boy to be able to have the fruit there would be a need for the legend of Nika to already exist in some form for the fruit to exist. Making two Nikas (Luffy and Joy Boy) plus the original legend
1- In the deep past: The Legend of Nika start (Pehaps among a specific race like thr Lunarians), the belief of this people in this entity make the fruit "manifest"
2 - Void Century: The worship of Nika is at it's peak, Joy Boy eat the Nika fruit, after this the WG work to supress anything related to Nika
3 - Presen: Luffy eat the Nika fruit
That would be the three times, because for Joy Boy to be able to have the fruit there would be a need for the legend of Nika to already exist in some form for the fruit to exist. Making two Nikas (Luffy and Joy Boy) plus the original legend