It's a nice idea but I believe we considered it and decided against it a while ago. The trouble is that the proportions of compounds relative to each other doesn't matter, and vacuole storage space doesn't necessarily correspond with amount of a compound. The player is likely to have ten or more times as much of the simple compounds (oxygen, carbon dioxide, etc.) than the complex ones they're often more concerned about (amino acids, proteins, etc.), so they'll be looking at the smaller parts of the pie chart more often. Even if you hide the more common compounds in your design, what's left will still take up too small a proportion to make sense of at a glance.
This may be counteracted by another problem though: larger molecules take up more space in vacuoles than smaller ones, so in effect the storage space used for each may be about the same even if you have 10 oxygen and 2 amino acids.
I don't know what others' opinions on this are, but in my opinion the simplest solution as far as the player is concerned is to limit each vacuole to storing one type of compound. Then you can use bars or pie charts for each compound which are based on all organelles storing that compound, and you see clearly the most important things: the proportion of a compound you have relative to its maximum storage space and exactly how much of a compound you have, both at a glance. The player could set the compound for each vacuole in the editor, and the maximum number of units of a compound your cell can hold is found by dividing all that compound's vacuoles by the weight/size of each molecule.
But this is a concept the team created a while ago but now it annoys me and I feel like there's a better solution somewhere. Do cells in real life store multiple resources in one vacuole? If they don't it's fine, but even so that's not how vacuoles in the game now work. Plus, to store even the most basic compounds a cell would have multiple vacuoles. So maybe vacuoles should be general storage instead, the trouble then is working out how to reconcile that with the problems I mentioned above.
Also, pie charts aren't the best.