Nginx – Fixing ‘Too Many Open Files’ Error

This bug report seems to confirm your initial suspicion:

This is the wrong answer to the question "how do I set ulimits for a daemon process?" /etc/security/limits.d is only processed by pam_limits, which has no reason to be in the path for service startup.

On manual restart, on the other hand, nginx is inheriting the limits from your shell.

The workaround: just call ulimit in the nginx initscript. You can't use ulimit -n as a regular user, but the init script should have enough privileges when being run on startup.

Add the following line to your nginx and restart the process:

worker_rlimit_nofile 30000;

This will allow the workers to take on more files. You can then verify with:

su - nobody
ulimit -Hn
ulimit -Sn

This should output the new hard/soft limits.

Reference