This confirms my theory. Custom tracks were made taking care about the 3ds limitations (hardware, NTR, OS). However, with Luma's new Rosalina menu, which runs as a another system module in the background, it's making the game lag. I've checked myself with Luma 8.0 vs Luma 7.0 and the first one lags.
@Aurora Wright,
@TuxSH I beg you, add a SVC that allows disabling Rosalina, just for compatibility with homebrew which was almost lagging, but now does. All the current custom tracks were made in a time period of 3 years, and remaking them again to remove the lag is just a nope. Either that, or a safe way to terminate Rosalina's thread.