Firmware: One For All
Similar to other NAS device manufacturers, Qnap offers a single firmware for all devices in a given product line. This has the advantage of allowing the firmware to be easily adapted to the different models, since both the hardware and the features are almost identical anyway. The differences are mostly in the details, for example the missing eSATA management menu item on a device without eSATA ports.
Because the TS-459 Pro and TS-559 Pro are based on identical hardware (except for the additional drive bay in the 559 Pro), the biggest differences in the Web-based administration interface are the hard drive identification and RAID mode management menus, with the TS-559 Pro simply allowing for the configuration of one more hard drive. Settings like the choice of file system or RAID mode are the same.
Pretty much all that remains when comparing mostly-identical NAS devices is the assumption that the fifth drive in the TS-559 Pro gives it some kind of performance advantage compared to the TS-459 Pro.
RAID In Theory
The choice of RAID mode and the question of whether the device is mostly going to be used for read or write operation are both relevant. Using a dedicated RAID controller and multiple drives produces a solid performance increase using RAID 5, if you're most concerned about read data rates. RAID 0, 1, and 6 modes also benefit from increasing the number of hard drives for read operations. However, the specific transfer rate increase depends on other factors as well: stripe size, the number of I/O requests, and whether they are sequential or random, not to mention the hard drives you are using. Pretty much the same factors play a role in affecting write performance, although things get a bit more complicated.
The vast majority of NAS devices for the consumer market lack a dedicated RAID controller for managing XOR operations, and that goes for the TS-459 Pro and TS-559 Pro as well. XOR is the basic mathematical operation to create (or restore) data redundancy for an array. These operations are handled by the dual-core Intel Atom D510 CPU instead (also known as host-based RAID), which can have a somewhat limiting effect on RAID array performance.
Take a look at the following pages to find out whether the additional disk in the TS-559 Pro has any effect on transfer rates, and if so, how much.