I believe Nintendo is moving in this direction, mostly since there are no Zoras present in Phantom Hourglass or Spirit Tracks. But the original Zora design from LoZ are there under the name Geozard. Some of which even breathe fire like the original Zora/River Zora of the older games.
They look very similar to the original concept of the Zora before they were made into the peaceful tribe in OoT. Another point is the Gorons have been present in PH and ST so Nintendo is not dropping all the species of OoT, some are staying around. WW gave the explanation that the Zora "evolved" into the Rito. So it might be possible that there were never very many Zora in the world or they were only the single very small isolated tribe built around Jabu Jabu just as the entire Rito species is settled around Valoo. And the Kokiri/Koroks lived around the guardianship of the Deku Tree.
The Zora were still known, or at least Hylians knew of them in PH since there were the treasures Zora Scale and Ruto Crown, the Ruto crown mentions the princess of the Zoras but by that point in time it could be a local legend surrounding the item.
In three consecutive sequels there have been no Zora, which lead me to believe that they no longer exist as Zora in that specific point in the timeline. The only evidence to back this up though is just the description that the Rito were once Zora, and after that they have never appeared again. Meanwhile Nintendo has reused them again in the separate timeline in TP. So it seems that After the great flood they no longer exist, but in the world without the great flood they are still around.