Some spoilers below about Nanaki's past:

Yeah the only one who ever makes a reference to Nanakai being the last of his species is...Nanaki himself. But Bugenhagen makes references that there are others like Nanaki somewhere in the world.

As for Nanami's mother, the Gi tribe attack is probably the best guess. I don't think it was mentioned about his mother at all. Just that 40 years ago the peaceful tribe living in Cosmo Canyon is attacked by the violent Gi tribe. Seto, Red's dad, protects the Canyon by going through a secret passage, and succeeds in holding off the Gi tribe, but in the end is pierced by their petrifying arrows and turns to stone. The Canyon tribe, including Seto's son, Nanaki, believes Seto turned tail and fled. Only Seto's father-in-law, Bugenhagen, knows the truth.

Then, 500 years later, Red XIII and his grandchildren climb to the top of Cosmo Canyon and look at the ruins of Midgar, now covered in greenery and forest.