If the player listens to the Pokégear radio while near or inside the ruins, they will hear strange noises generated by it on channel 13.5. In Pokémon HeartGold and SoulSilver, the player must be inside one of the chambers and any channel on the radio will broadcast the noises. Some of those noises are actually Ho-Oh's distorted cries, and the melody of the Azure Flute.
Source: Bulbapedia/ Ruins of Alph
They serve no real purpose. Maybe they are there to add to the eeriness of the place.