All the completed ones were destroyed, there is nothing to say that others were not built. I can see 2 scenarios, some Shadow Omegas were not complete in time to face the Whitestar fleet. After the active ones were destroyed, Clarke's supporters realised they were on the losing side and jumped the unfinished Shadow destroyers to a covert location for completion at a later date.neko said:War level on the other hand is at least offering you a ship that's meant to fight. If you're fighting in 2261 at least. After which they're all destroyed...
Alternatively, someone could have copied the technical data and used it to construct more at a later date. In fact this is the more likely scenario. We know that some shadow tech survived as it was the basis the for the Nemesis.
Just because all the Shadow Omegas that were functional in late 2261 were destroyed does not mean that they were the only ones ever built.