Why did Apple delete my stocks list from the Stocks app?

I assure you that Apple did not delete your stocks list, as Apple has no access to your phone whatsoever. So you need to troubleshoot the issue.

• To start with, did you sync stocks to iCloud or not? Go to Settings, tap on your name, then iCloud. Is Stocks turned on?
• If you did not turn it on then the Stocks will be in your latest iCloud or iTunes backup made before they disappeared. Restoring the backup will restore the list. Note that it will overwrite everything on your phone, not just Stocks. If it is on then the backup will not contain your stocks, BTW.
• If the Stocks switch was turned on, do you share an Apple ID with anyone? If it was, and they deleted the stocks from their phone it would be deleted from yours also. And in that case there is no way to get them back. Which is just one of many reasons not to share an Apple ID.
• It could be that your phone's storage is corrupted; in that case you must restore the phone to factory settings (Restore your iOS device to factory settings - Apple Support), then restore your most recent backup that contained the stocks list. (Restore your iOS device from a backup - Apple Support)
• Did you do anything unusual just before they disappeared? Updated iOS? Restored iOS? Restored a backup? Added a stock? Deleted a stock?

The stocks which you've selected would be part of your backup, maybe restore your most recent backup to recover them (but note that you'd lose any changes on your iPhone since your last backup).

Edit: If you're syncing Stocks to iCloud, then the parameters would not be in your backup.

No, Apple did not remove the tone that you paid for from your phone. However, tones are not stored on the phone through a reset, so they need to be restored from iTunes.