Dram

# Support Clean (aka Search Engine Friendly) URLs
location / {
try_files $uri $uri/ /index.php?$args;
}

nginx: the configuration file /etc/nginx/nginx.conf syntax is ok
nginx: configuration file /etc/nginx/nginx.conf test is successful
user www-data;
worker_processes auto;
pid /run/nginx.pid;
events {
worker_connections 2048;
use epoll;
}
http {
server_tokens off;
client_max_body_size 100m;
charset utf-8;
client_body_timeout 10;
client_header_timeout 10;
reset_timedout_connection on;
keepalive_timeout 90;
keepalive_requests 100;
proxy_read_timeout 120;
proxy_send_timeout 120;
include /etc/nginx/mime.types;
sendfile on;
tcp_nodelay on;
tcp_nopush on;
server_names_hash_bucket_size 2048;
server_names_hash_max_size 2048;
map_hash_bucket_size 2048;
map_hash_max_size 2048;
ssl_stapling on;
ssl_stapling_verify on;
ssl_trusted_certificate /etc/ssl/certs/ca-certificates.crt;
ssl_session_cache shared:SSL:100m;
ssl_session_timeout 1h;
ssl_session_tickets on;
ssl_session_ticket_key /etc/nginx/sites-conf/ticket.key;
access_log off;
error_log /var/log/nginx/error.log;
gzip_static on;
gzip on;
gzip_comp_level 6;
gzip_types text/plain text/xml application/json application/xml application/x-javascript text/javascript text/css text/json;

fastcgi_cache_path /var/cache/nginx/site levels=1:2 keys_zone=site:10m max_size=128m inactive=24h;
fastcgi_temp_path /tmp/nginx 1 2;
fastcgi_cache_key "$request_method|$host|$request_uri";
fastcgi_ignore_headers "Cache-Control" "Expires";
fastcgi_cache_min_uses 1;
fastcgi_cache_valid 200 301 302 304 3h;
fastcgi_cache_use_stale error timeout invalid_header http_500;

include /etc/nginx/sites-conf/site.conf;
include /etc/nginx/conf.d/*.conf;
include /etc/nginx/sites-enabled/*;
server {
listen *:80;
server_name 90.100.08.08;
access_log /var/log/nginx/phpmyadmin.access.log;
error_log /var/log/nginx/phpmyadmin.ru.error.log;
index index.php;
root /usr/share/phpmyadmin;
location / {
try_files $uri $uri/ /index.php?$args;
}
location ~ \.php {
try_files $fastcgi_script_name =404;
fastcgi_pass unix:/run/php/php7.2-fpm.sock;
fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
include fastcgi_params;
}

location ~ \.(tpl|xml|log)$ {
deny all;
}

location ~ /\.(git|svn|hg|bzr) {
deny all;
}
}
}
types {
text/html html htm shtml;
/////тут я сократил ибо не влазило на форум
}
server {
server_name site.ru www.site.ru;
listen 80;
rewrite ^(.*) https://$host$1 permanent;
}
server {
listen 443 ssl http2;
server_name site.ru www.site.ru;
if ($host ~* www\.(.*)) {
set $host_without_www $1;
rewrite ^(.*)$ https://$host_without_www$1 permanent;
}
ssl_certificate /etc/ssl/certs/site_ru.crt;
ssl_certificate_key /etc/ssl/private/site.ru.key;
resolver 8.8.4.4 8.8.8.8 valid=300s;
resolver_timeout 10s;
ssl_protocols TLSv1 TLSv1.1 TLSv1.2;
ssl_ciphers 'ECDHE-RSA-AES128-GCM-SHA256:ECDHE-ECDSA-AES128-GCM-SHA256:ECDHE-RSA-AES256-GCM-SHA384:ECDHE-ECDSA-AES256-GCM-SHA384:DHE-RSA-AES128-GCM-SHA256:DHE-DSS-AES128-GCM-SHA256:kEDH+AESGCM:ECDHE-RSA-AES128-SHA256:ECDHE-ECDSA-AES128-SHA256:ECDHE-RSA-AES128-SHA:ECDHE-ECDSA-AES128-SHA:ECDHE-RSA-AES256-SHA384:ECDHE-ECDSA-AES256-SHA384:ECDHE-RSA-AES256-SHA:ECDHE-ECDSA-AES256-SHA:DHE-RSA-AES128-SHA256:DHE-RSA-AES128-SHA:DHE-DSS-AES128-SHA256:DHE-RSA-AES256-SHA256:DHE-DSS-AES256-SHA:DHE-RSA-AES256-SHA:AES128-GCM-SHA256:AES256-GCM-SHA384:AES128-SHA256:AES256-SHA256:AES128-SHA:AES256-SHA:AES:CAMELLIA:DES-CBC3-SHA:!aNULL:!eNULL:!EXPORT:!DES:!RC4:!MD5:!PSK:!aECDH:!EDH-DSS-DES-CBC3-SHA:!EDH-RSA-DES-CBC3-SHA:!KRB5-DES-CBC3-SHA';
ssl_prefer_server_ciphers on;
ssl_dhparam /etc/nginx/sites-conf/dhparam.pem;
add_header Strict-Transport-Security "max-age=63072000; includeSubdomains; preload";
add_header X-Content-Type-Options nosniff;

access_log /var/log/nginx/access.site.log;
error_log /var/log/nginx/error.site.log crit;
root /var/www/site;
index index.php index.html index.htm default.html default.htm;


location ~* /(images|cache|media|logs|tmp)/.*\.(php|pl|py|jsp|asp|sh|cgi)$ {
return 403;
error_page 403 /403_error.html;
}

location ~ \.php$ {

include fastcgi_params;
fastcgi_cache site;
fastcgi_buffers 16 16k;
fastcgi_buffer_size 32k;
fastcgi_index index.php;
fastcgi_read_timeout 30;
fastcgi_pass unix:/run/php/php7.0-fpm.sock;
fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;

set $nocache $cookie_joomla_user_state;
if ($request_uri ~ /index.php)
{
set $nocache 1;
}
if ($arg_cached = "1")
{
set $nocache 0;
}
fastcgi_no_cache $nocache;
fastcgi_cache_bypass $nocache;
}

location ~* \.(js|css|png|jpg|jpeg|gif|swf|xml|txt|ico|pdf|flv)$ {
valid_referers none blocked server_names ~(site|yandex|google|yahoo|bing|facebook|mail|rambler|nigma|ask|bing);
if ($invalid_referer) {
return 403;
}
error_page 404 = @fallback;

rewrite ^/components/com_jcomments/js/extcomm-widget.js /media/com_comments/raw/js/widget.js;
expires 7d;
}
}
fastcgi_param QUERY_STRING $query_string;
fastcgi_param REQUEST_METHOD $request_method;
fastcgi_param CONTENT_TYPE $content_type;
fastcgi_param CONTENT_LENGTH $content_length;
fastcgi_param SCRIPT_NAME $fastcgi_script_name;
fastcgi_param REQUEST_URI $request_uri;
fastcgi_param DOCUMENT_URI $document_uri;
fastcgi_param DOCUMENT_ROOT $document_root;
fastcgi_param SERVER_PROTOCOL $server_protocol;
fastcgi_param REQUEST_SCHEME $scheme;
fastcgi_param HTTPS $https if_not_empty;
fastcgi_param GATEWAY_INTERFACE CGI/1.1;
fastcgi_param SERVER_SOFTWARE nginx/$nginx_version;
fastcgi_param REMOTE_ADDR $remote_addr;
fastcgi_param REMOTE_PORT $remote_port;
fastcgi_param SERVER_ADDR $server_addr;
fastcgi_param SERVER_PORT $server_port;
fastcgi_param SERVER_NAME $server_name;
fastcgi_param REDIRECT_STATUS 200;
server {
listen 80 default_server;
listen [::]:80 default_server;
root /var/www/html;

index index.html index.htm index.nginx-debian.html;
server_name _;
location / {


try_files $uri $uri/ =404;
}
}
fastcgi_param QUERY_STRING $query_string;
fastcgi_param REQUEST_METHOD $request_method;
fastcgi_param CONTENT_TYPE $content_type;
fastcgi_param CONTENT_LENGTH $content_length;
fastcgi_param SCRIPT_NAME $fastcgi_script_name;
fastcgi_param REQUEST_URI $request_uri;
fastcgi_param DOCUMENT_URI $document_uri;
fastcgi_param DOCUMENT_ROOT $document_root;
fastcgi_param SERVER_PROTOCOL $server_protocol;
fastcgi_param REQUEST_SCHEME $scheme;
fastcgi_param HTTPS $https if_not_empty;
fastcgi_param GATEWAY_INTERFACE CGI/1.1;
fastcgi_param SERVER_SOFTWARE nginx/$nginx_version;
fastcgi_param REMOTE_ADDR $remote_addr;
fastcgi_param REMOTE_PORT $remote_port;
fastcgi_param SERVER_ADDR $server_addr;
fastcgi_param SERVER_PORT $server_port;
fastcgi_param SERVER_NAME $server_name;
fastcgi_param REDIRECT_STATUS 200;

include /etc/nginx/mime.types

Оптимизайка:
Dram, вы не вес, а скорость выполнения запроса с разной длиной varchar проверьте, если это поле участвует в условии where, group by или order by. Особенно если в плане по этому полю предлагается filesort.