Why should wooden warehouses have more capacity than the plaster version? If you're just looking for a reason to build them over plaster - how about the fact they don't take clay? Clay is easy to get on servers that stop people from claiming clay deposits and/or refill them periodically, but I imagine it will be a fairly precious resource in the MMO (not that that technically makes much sense, as we should be able to easily get clay from any beach). But giving different capacities to two buildings with the exact same footprint and model doesn't make much sense to me.
Due to the window size limitations, you shouldn't be using a warehouse to store anything but super heavy stuff, like large quantities of ore or cut wood. In that case, the unbalanced capacity is still an issue.