1 thing I noticed is that the problem is that nginx is running as dhapache user and inherits different set of limit. Reboot didn't help for that.
In /proc/pid/limits for nginx I can see:
[ps126641]$ cat /proc/19381/limits
Max open files 1024 1024 files
for processed running under my account:
[ps126641]$ cat /proc/29907/limits
Max open files 132384 132384 files
Which is what I set in /etc/security/limits.conf.
- soft nofile 132384
- hard nofile 132384
Do you know how to bump that for dhapache user as well?