You can choose either keeping them enabled or not. Disabling them of course makes you save time, but it's not a must. The only difference is that the timer starts whenever you gain control of Coco's plane (fade-in of the level, as soon as it fades in you gain control). Everything else follows the normal NIG rules. You can either disable sfx by pausing, then go to the warp room after disabling them, or disable them as you would do in a NIG run after entering a level in warp 1. Your choice.

Disabling sfx makes you skip all cutscenes instantly in every category. Also, you can start the timer whenever you want, but mods will anyway add the time you spent inside Bye Bye Blimps when approving your run in the leaderboard, because the rules state that the timer starts as soon as you gain control of Coco in that level.