You have 2 separate drives.
One with your operating system (and usually all your programs) and the other drive is for storing data (example - Folders with music and video) This is so the operating system starts almost instantly (no waiting times) and your can open programs just as quick. Wheres as the stored data, under normal, run of the mill, use, generally only needs to be accessed at a slower rate from a big storage drive. Professional usage may require fast access, but they have high end set-ups to utilize it.
The majority of flash drives ( whether sata, msata, m2 or PCD-E) are 1TB or more commonly smaller, yet it is easy to find hard disk drives a lot larger (up to 6TB). Price has a lot to do with the set up you mentioned. Look up the price of normal (not talking about high end or enterprise drives) 4 TB hdd and compare it to a good, normal 500gb SSD and see which is more expensive.