Having a D parition on the same hard disk as the C parition is pretty pointless if you are seeking to secure your files from annihilation.
In most circumstances I'd agree; where it can be useful though is in those rare situatons where the OS is irrecoverably screwed (I've had this once with a particularly horrible malware infection) or the owner wants for format the disk for other reasons.
This was a bigger deal historically, where Windows might have had a lifespan of twelve months before it was so monumentally buggered that 'format it and start again' was deemed acceptable preventative maintenance, but there are situations where it can be useful.
You're right though, in terms of "safeguarding your data" it's largely pointless. I blew away the OEM partitioning on my laptop in favour of one big one for exactly that reason.