a few months back I was running an assessment and found an issue that identified the cause of some slow SQL query performance on Configuration Manager. An article has been released in regards to both SQL 2014 and SQL 2016 that shows Configuration Manager may run better when the site database is configured at a different SQL CE compatibility level.
I wanted to point it out to those that may have missed it, as it may not be obvious which was the case with my customer who did a fresh Install to SQL 2014 when they moved to 2012. Which meant the slow SQL queries were not so obvious as they may have been had they gone directly to SQL 2012 and then upgraded to SQL 2014 at a later date.
In my customers case we ran tests and found that the performance increase went from 45 seconds to 16 seconds.
Here is a link to the article which is pretty self explanatory and has some SQL queries you can run to test and see if you’re experiencing some slow SQL query times.
I hope this helps you out