Couple of things to ponder and look into....
First, on my Linkstation LS441d, when files are deleted they go to a folder called Trashed. I know you said in your post that you disabled the recycle bin feature, but there might be still be a resident trash folder that deleted files are accumlating in.
Second, there's an older piece of software called StepTree (my favorite) and another software called Windirstat. Both will scan your drive, folder, network share, or whatever in your file system hierarchy you select and visualize it in 3d chunks. It's an incredibly useful way to see what's taking up all the space.
Third, and this is pure speculation, maybe there is something wrong with your software, fs, storage controller or even hard drives, that is preventing data from being marked as deleted....maybe it's storing and not deleting. If you have no data on the array, you could try removing individual hard drives and testing them. That way you can rule out hardware.
Fourth, try upgrading your device firmware to the latest. The issues you describe might be a bug from an older version.
Fifth, if the option exists, try formatting or creating your partitions using a different file system (xfs vs ext, for example).
