The difference between the red and blue treasure chests are:
Red- contains items that will disappear after use suce as Gumi(or Gels, as they were called in ToS) and bottles
Blue - contains items for equipping, such as Weapons and Armors
Note: If you have 15 of the same item, you will not be able to acquire another one from the treasure chests. Also, you will not be able to throw away any items.
Note2: You are also able to discover items from the background in towns. Constantly tap on the circle button if you want to make sure that you acquire each of them.