Bluetooth or wired headset? a google seems to show a handful of results at varying times over the last couple of years about crackly audio on fortnite on switch, but it doesnt seem like it's a systemic issue.
Have you tried checking the port for lint or other debris? blow hard into it, see if the crackling is worse if you spin the headphone jack while it's connected.
Doesnt seem like Fortnite has any other audio options, on PC you can turn the audio quality down, i assume switch doesnt have an equivalent setting?