the game is probably just running too slow so there will always be a pause between the frames where there's no audio, hence the crackling. Look at the average frametime, if it's above 1/60s (16.6666…ms) it means that the game is running too slowly. You can try overclocking the processor, otherwise you can also wait for new updates with more optimisations.Melonds is still not running properly for me, and I’m wondering what you did. When I launch a DS game, the audio is distorted and the game is running very slowly.
Did you place the melonds file at the root of the SD? Did you have to modify any Switch settings?