Hey there, Omga4000!
To answer your question: Frankly, yes, it really does matter what you put in your NAS!
WD Red drives are specifically designed for NAS/RAID environments. What makes them different from all the rest drives is that they have the specific TLER feature (time-limited error recovery) which prevents HDDs from being dropped off the array due to extended error recovery.
This is something that regular HDDs that are not equipped to do and generally fail in such environments.
This also provides more availability and less down time rebuilding the RAID/NAS.
They have the NASware 3.0 firmware which also differentiates WD Reds from regular desktop drives. With this you get SMART command transport support (SCT), power management support, lower power consumption, etc. WD Red drives are also tested to run 24/7.
http://www.wdc.com/en/products/products.aspx?id=810
You mentioned WD Green drives, so I will do my best to draw the differences. WD Greens are a reliable secondary storage solution. They also have lower power consumption and they run cooler and quieter than most drives. But not really designed for NAS environments. They are recommended for secondary storage, as I already mentioned as well as a reliable back-up in external enclosures and not really to be accessed regularly.
http://www.wdc.com/en/products/products.aspx?id=780
WD Purple drives are specifically for surveillance storage and security systems up to 8 bays and optimized for 32 HD cameras. They can run 24/7 indeed, but their purpose is totally different.
http://www.wdc.com/en/products/products.aspx?id=1210
The purposes of the drives are there for a reason. Basically, if you don't use them accordingly, you won't be able to experience their advantages and features. Not to mention that sometimes unsupported usage can void their warranty.
Hope I was able to clear things out for you!
If you have more questions, feel free to ask!
SuperSoph_WD