The problem is that they are stored there temporarily so they are still part of the system as they will be used at a later time. Even if they would be in the WAR the actual costs would be relatively low except for basic products like ores or minerals that need a lot of storage for little worth. And removing those will have negative consequences for market stability.
For example 1k LST is ~3000t which is 600 cost per week for wares ~150k worth which means 0,4% of its worth get lost per week (for FEO it would be ~1% + again for FE). These storage costs will be put on top of the normal price by the people selling it so the prices of basic goods will rise ~1-10% and swings will be wider because market making bigger stacks will be placed further up to compensate for storage fees.
However it would be a different topic if there would be a cheap storage like a tonnage uncapped (only volume counts) WAR for minerals, ores, elements, metals and alloys. Then you could make it so that every order just becomes a black mistery square in the CX WAR and even increase the fee for the normal WAR.