I have found EndNote X9.3.1 to be astonishingly faster: my library has 54K entries, almost all with PDF attachments and is decades old (started with EndNote 2). I previously switched to Windows because of poor performance on macOS, but now, the macOS version runs circles around the Windows (X9.2) version and is appreciably faster than Bookends on macOS.
Could this be a local issue? One thing I do is to keep my (larger) EndNote library(-ies) out of the iCloud-backup folder that can slow things on macOS. EndNoteSync can effectively back up your database. As a precaution, I use rsync (runs in the macOS terminal and there are plenty of YouTube tutorials) to back up my EndNote libraries with ease. You can even create cron (another handy Unix utility) tasks to do this periodically.
I could not be happier with the newest macos update.