I had just upgraded from domain mapping plugin 184.108.40.206 to 220.127.116.11 and noticed a large jump in database CPU usage.
Other users have reported the same slow query issue: https://premium.wpmudev.org/forums/topic/domain-mapping-has-got-too-many-rows
The reason is that on every page load domain mapping plugin is running a show tables query, my database has over 100,000 tables and this is causing a lot of unnecessary load.
Query monitor defined the following files and line numbers as the problem:
Domain mapping version 18.104.22.168 does not appear to use this query, and also showed markedly lower CPU usage.
The extra CPU load is actually high enough that I had to upgrade my server costing me hundreds of dollars per month... Since WPMUDEV is targeted towards multisite networks, I hope your developers will address this asap.