Yes, Hook stores its data where you’d expect: ~/Library/Application\ Support/com.cogsciapps.hook/. See also How to Backup and Restore Hook Data – Hook.
At this point auto deletion of bookmarks is a challenge because Hook is designed to enable you to add and remove entire file systems (like disk images, cloud shares, network mount points, version control systems, etc.) and to share across your Macs and with other people. However, the entries are lean. And we optimize as development progresses. (We also remember the old days of macOS, each release from 10.0 or so onwards would get leaner and leaner.)