To store the files on disk I keep directories marked by topic/year/month/day. The topics are stuff like taxes, finances, bills, etc. The important documents are in a couple encrypted HDDs that I use for backups. I've been thinking of doing an offsite storage like Backblaze B2 but it's probably overkill.
After scanning stuff in, everything gets shredded. There usually aren't many things to save but once they've been scanned they're there forever.
[0] https://www.amazon.com/Fujitsu-ScanSnap-iX500-Duplex-Scanner...