The root of a file geodatabase is a directory, and hardlinks aren't allowed on directories. Hardlinking individual files between separate file geodatabases will definitely cause corruption of one or more of the geodatabases, it would be a matter of when and not if.
If you have lots of duplicative geospatial data, it is better to change your workflows and practices to reduce the duplication than relying on filesystem-level functionality that is completely unaware of the filesystem structure of geospatial data.
Storage isn't free, and it can definitely add up in cost if mindlessly wasted, but in general the price of strorage pales in comparison to the cost of collecting or deriving data.