yes it would be worth it just to see if that is the problem
i have always been a fan of substrate but run with none now
if you have fauna that turn it over it is good
but without, it can be an organic waste trap
remember when you remove it you are changing the balance of bacteria in the tank
preheat some new salt mix for water changes afterwards
personally i would remove 1/2 the substrate then the other 1/2 a week later