1) Can mods be applied to current playthroughs or must fresh ones be started?

 

2) How easy or hard would a mod be to remove store owners at night?

 

I notice some like the jeweler in Serpent's Crown disappear at night, however must stay there.

To the first question, it depends on the mod but generally speaking you can add a mod to a game in progress with no problems. To the second question... hmm no idea

There is some structural information about NPC schedules in ScheduleGameData objects, but unfortunately the details of what a particular NPC does during each time slice are defined on the Unity data for that character and are hard to modify.