After you defeat Wallace you have access to all of the hidden DexNav Pokemon. Here are all of the ones from generation VI and their respective locations.
Skrelp - Routes 105, 106, 107, 108, 109 (Omega Ruby only)
Clauncher - Routes 105, 106, 107, 108, 109 (Alpha Sapphire only)
Klefki - Route 113
Phantump - Petalburg Woods
It's true that there aren't many at all, but this is because the hidden DexNav Pokemon's purpose was for players to be able to capture almost every Pokemon and complete the PokeDex with only Gen VI games, and, well, X and Y exist, so it would be largely unnecessary. Nevertheless, they put some in, at least!
Source: Serebii.net (http://www.serebii.net/omegarubyalphasapphire/dexnav.shtml)