Spindles don't scratch discs, people do.
Yeah, you could qualify a statement about spindles with "if you look through the discs a lot" and it would be more accurate. There's just a greater chance of scratches when a person handles a stack of loose discs.
It's a fine way to store discs that you don't plan on taking out often (or if you keep them fully stacked). These things were designed to have discs removed and used somewhere else. A box is better because there's less chance of dust or junk getting in between the discs...or if you have a covered spindle.
That being said, I'm pretty accident prone and, therefore, overly cautious with stuff.
EDIT:
To be fair, anything you handle a lot has a higher chance of scratchery. There are just more games involved with spindles/boxes. Where as with single cases you are only dealing with 1-2 discs.