Basic: A portion of the crystal stocks will be stored here safe from plundering. The Den does not expand the overall storage capacity.
Detail: The capacity of the Crystal Den shows how much crystal is protected from plundering. The better the Den is upgraded, the more resources can be protected from attackers. Espionage probes are able to detect the upgrade level of a Den as well as the amount of hidden resources. The storage capacity is not expanded as a result of the Den.