I'm having problems with PHP-FPM 5.6.28 reaching 100% cpu load for a few minutes. My server is Amazon EC2 m3.xlarge and the number of concurrent users is only 15 to 35.
Your problem doesn't indicate any issue with net.core.somaxconn settings.
It seems more like a problem caused by some bad php-mysql code.
As your CPU is 100% already, more PHP processes won't help.
The article is meant for servers where PHP can't accept more connection even before CPU is reached 100%.