Their sprites were molested into the game by a certain Glitch Pokémon (You know who - That famous Glitch from Generation I).
Let's be serious now, Hilbert/Hilda is looking for N, and N is looking for Hilbert/Hilda, as said before.
Time to think about it. Below is a silly theory and very illogical.
Red was on Mount Silver.
Then, Ethan/Kris beat Red and Red got out of Mount Silver.
So now Ethan/Kris was on Mount Silver.
Then, as soon as Brendan/May finished, they just, I don't know, VANISHED or something?!?!
But after Lucas/Dawn finished too, they could have even went to Stark Mountain, Spear Pillar, or vanished themselves too.
Hilbert and Hilda came across Mount Silver while searching for N. They lost a Double Battle against Red and Ethan/Kris. So then they whited out, and then it would be unknown where they (Hilda + Hilbert) were.