99 out of a 100 times this is a plugin or theme issue.
Some rubbish off of ThemeForest that bloats the database... Plugins storing enourmous log files or in other ways doing inefficient queries and bogging down the db...
Also, WooCommerce is getting better by the hour, but still is somewhat poorly made and could use some major optimization.
So usually this is poor work on devs of themes/plugins that create these "killing queries".
I would never recommend W3TC, since it was abandoned by developer and left with some serious issues. I think its in some form of development today (maybe someone has taken over and doing bits on it), but we would never dare using it for production sites or client work. (Looking very much forward to trying Breeze out, on a sidenote)
I have quite a bit of experience in this field, and I'm sorry to say that generally its the crap installed on your site that is the issue
We see this in lots of commonly used plugins. Just to name a few that we blacklist due to performance or cluttering issues:
- Autoptimize (or whatever that minimization plugin is called...)
- Yoast SEO
- Monster Insights (and most other Google Analytics plugins)
There are so many of these "big name" plugins that are actual junk, and destroy your site/db efficiency.
Apart from that, when the daily backups run on Cloudways its a huge resource hog (they really need to work on this). We run a farm of Kyup servers, and everyday when a backup runs it autocales and adds 1gb of ram and 1 more cpu core just to do the backup, and before we switched to Kyup we'd see db crasches. So there is a chance that this is your issue as well.
But... If you have a cheap themeforest theme or similar, and several plugins installed, and you're running this on a low-level server (such as 1gb/1core or similar) then this is probably your issue.