/etc/security/limits.conf soft nproc limit appears to be ignored
Check the file /etc/security/limits.d/90-nproc.conf as this is likely overriding your settings. I wrote about this exact same issue last year http://scott.cm/max-processes-1024-limits-conf/
You could try to change the ulimit value at the beginning of the script, which is launching the mongodb database.
A child process inherits the resource limits from the calling process.