I posted my concern about this in comments to Bug 30145 - themes : Yahoo skin account name & quota area but I also want to bring it up in the forum.
In brief, unless I'm missing something, Zimbra Desktop only tells you how much space you're using in your account; it doesn't tell you what your quota is or the relative percentage used.
In a business/education environment, I would expect many hardcore Zimbra users eventually to migrate to ZD and to use the web client rarely. This would especially be the case for laptop users who'd probably want to have a single, consistent interface that allowed them to work offline. But the local storage capability of ZD would also be a selling point for users of desktop workstations.
However, since ZD doesn't give any feedback on relative quota usage, I can foresee users filling up their accounts unawares, leading to IT headaches as people come asking why they aren't getting their mail, or why mail to colleagues is bouncing. While ZCS autogenerates a quota warning after a certain threshold, these are easily ignored or left "for later", then forgotten.
I can wait until ZCS 6.0, but I would just like to make sure that ZD users will have access to their quota usage without having to log into the web client.