This weekend I reached the breaking point with my laptop (MacBook Pro, 15", 2016). For a few months now I've been having random long-spinning beachballs when launching applications or doing any sort of disk-heavy IO. I upgraded from High Sierra to Mojave hoping that would fix it, but there was no change.
I finally did another round of Googling about my problem this weekend, and I found a few threads by people that seemed to be having the same trouble I've been having.
The main symptom is that, after running Disk Utility's First Aid tool, you're given a message like this:
... Snapshot is invalid. The volume /dev/rdisk1s1 could not be verified completely.
This was the case even when running Disk Utility in recovery mode.
This site purports to have a "solution" for the problem, but that solution is reformatting the drive. Across other results (from Reddit, Google, Stack Exchange, etc.) the verdict seemed to be that if you want to ensure that this problem goes away, reformat your drive.
This Windows 95 sort of solution feels crazy, but I have enough backups around that I went ahead and tried it anyway. Nothing else was working, and I figured this had the best chance of fixing things.
It took about 45 minutes to wipe the drive and have Mojave reinstalled on it, and another couple of hours of restoring files from backups, but my laptop feels so much faster now.
I haven't found any detailed technical documentation to better understand what is actually going wrong with the filesystem in this instance, and I hope Apple addresses whatever sort of bugs are causing this so that no one else has to go through this. But, if you find this and you've tried everything else, my advice to you is to just bite the bullet and wipe your drive (after backing up)!