how to vertically expand a ReadyNAS 104

Vertical expansion:  expanding capacity by replacing smaller disks with larger ones

Horizontal expansion: expanding capacity by adding drives to empty bays.

So what you attempted was horizontal expansion, not vertical.  However, as you discovered, adding a second 3 TB drive doesn't expand capacity.  With XRAID, adding the second disk gives you RAID redundancy - protecting your data from a routine disk failure. That can't be undone without destroying your data.

The simplest solution is to purchase another 3 TB drive and put it into slot 3.  If you do that, your capacity will increase to 6 TB (~5.45 TiB). Adding a fourth 3 TB drive would give you 9 TB (~8.2 TiB) of total space. 

Your other option is to back up your data, do a factory reset on the NAS, set it up again in flexraid mode - creating two volumes (one for each disk).  Put some shares on each, and then restore your files from the backup.

Note it is possible to create a single 6 TB volume that spans both disks.  However, that is a risky thing to do.  When either drive fails you will lose all the data on the NAS.  With two volumes, you'd only lose the data on the failed drive.