There is a high propensity they might get scratched.
Hi jred. Welcome to the forum!
If a disk is used often, the propensity to becoming scratched is always present, regardless of how it’s stored. Storage on a spindle becomes particularly viable in scenarios where one is "archiving" the media for backup, as the OP conceivably would do. For disks that are used regularly, naturally it can be more convenient if the disk is individually packaged in its jewel case.
As for aesthetics, that of course is a personal preference. If "art work" (booklet that accompanies the CD) is a necessity, obviously that too has to be dealt with accordingly and can to a certain extent dictate storage options.
Invariably though, the larger ones collection of CDs becomes, the more compelling it becomes to find a solution that does not involve jewel cases. In fact, at some level when ones collection grows into the many thousands, one can become compelled to get rid of CDs altogether and instead just store the data on an external drive, in a compressed and lossless format.
Point is, for those with seriously large music collections, physical space and scalability of space is definitely an issue to be reckoned with.
Not to muddy the thread by going off topic, but this is a big reason I don’t have/use vinyl albums but use digital in the first place. Space!
And for those with the "Crème de la crème" in audio - reel-to-reel tapes - where 30 minutes of music is on media larger than a frisbee, typically these folks have relatively few reels (and hence not much music) or they are extremely wealthy and have significant dedicated "library" space.