There is a Dusk Stone in Team Galactic's HQ, and in an area of Victory Road only accessible after defeating the Elite Four. They can also be found with the Pickup ability.
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Dusk Stones cannot be found in any GBA game. Stones like this are exclusive to Diamond, Pearl, and Platinum. Likewise you can't find a dawn stone or shiny stone in any GBA game.
Iron Island.
you can find dusk stone's in swirling dust in cave's. (random stones/gems and the mole pokemon) and a veteran, south to a hiker, on route 10 will give you a dusk stone.
The first one is in the Galactic Warehouse in Veilstone City. You can also dig Underground for more Dusk Stones, as well as other elemental evolution stones!
You can find shiny stones on route 228 and Iron island