¿Cómo puedo mejorar el rendimiento de esta consulta de Joomla?

I don't know why you need the calc_found_rows, but left it in there. As for the query, since all your group_concats were mostly against the profile table and optionally the user groups, I did a prequery (via tmpGrpCat alias) that just did the users with their corresponding group_concat and max() for elements such as email, condice..., cell, etc. I also included in this pre-query to exclude where the profile value was not "" as that would appear to be consistent across the board for your interested values.

I then did a simple left-join on the users table to get their id/name and the rest of the aggregates. This should simplify the engine to run through all the records ONCE for each of the profile_key LIKE (or equality) conditions once, group them by user's ID, then have it ready to go for the outermost query.

If this works, let us know performance improvement. If also can help others with performance techniques in future too.

SELECT SQL_CALC_FOUND_ROWS
      a.id,
      a.name,
      coalesce( tmpGrpCat.email, '' ) as email,
      coalesce( tmpGrpCat.codice_agente, '' ) as codice_agente,
      coalesce( tmpGrpCat.codice_agente_fisso, '' ) as codice_agente_fisso,
      coalesce( tmpGrpCat.codice_agente_VAR, '' ) as codice_agente_VAR,
      coalesce( tmpGrpCat.cellulare, '' ) as cellulare,
      coalesce( tmpGrpCat.AgTitle, '' )  as Agenzia,
      coalesce( tmpGrpCat.RuoloTitle, '' )  as ruolo,
      coalesce( tmpGrpCat.Canale, '' )  as Canale,
      coalesce( tmpGrpCat.Area, '' )  as Area,
      coalesce( tmpGrpCat.Status, '' )  as Status
   FROM   
      joo_users as a
         LEFT JOIN 
         ( SELECT 
                 up.user_id,
                 GROUP_CONCAT( DISTINCT IF( up.profile_key LIKE 'profile.agenzia_%', b.title, NULL )) AgTitle,
                 GROUP_CONCAT( DISTINCT IF( up.profile_key LIKE 'profile.ruolo_%', b.title, NULL )) RuoloTitle,
                 GROUP_CONCAT( DISTINCT IF( up.profile_key LIKE 'profile.canale_%' AND up.profile_value = '1', 
                    REPLACE( up.profile_key, 'profile.canale_',''), NULL)) AS canale,
                 GROUP_CONCAT( DISTINCT IF( up.profile_key LIKE 'profile.area_%', 
                    up.profile_value, NULL))  AS area,
                 GROUP_CONCAT( DISTINCT IF( up.profile_key LIKE 'profile.status_%', 
                    up.profile_value, NULL))  AS status,
                 MAX( IF( up.profile_key = 'profile.email', up.profile_value, NULL) ) AS email,
                 MAX( IF( up.profile_key = 'profile.codice_agente', up.profile_value, NULL) ) AS codice_agente,
                 MAX( IF( up.profile_key = 'profile.codice_agente_fisso', up.profile_value, NULL) ) AS codice_agente_fisso,
                 MAX( IF( up.profile_key = 'profile.codice_agente_VAR', up.profile_value, NULL) ) AS codice_agente_VAR,
                 MAX( IF( up.profile_key = 'profile.cellulare', up.profile_value, NULL) ) AS cellulare
              FROM 
                 joo_user_profiles AS up
                    LEFT JOIN joo_usergroups AS b 
                       ON REPLACE(up.profile_value, '"', '') = b.id
                    WHERE
                        ( up.profile_key LIKE 'profile.agenzia_%'
                       OR up.profile_key LIKE 'profile.ruolo_%' 
                       OR up.profile_key LIKE 'profile.canale_%'
                       OR up.profile_key LIKE 'profile.area_%' 
                       OR up.profile_key LIKE 'profile.status_%'
                       OR up.profile_key = 'profile.email'
                       OR up.profile_key = 'profile.codice_agente'
                       OR up.profile_key = 'profile.codice_agente_fisso'
                       OR up.profile_key = 'profile.codice_agente_VAR'
                       OR up.profile_key = 'profile.cellulare' )
                       AND up.profile_value != '""' 
                       AND up.profile_value != '"0"'
                    GROUP BY
                       up.user_id ) as tmpGrpCat
            ON a.id = tmpGrpCat.user_id
   ORDER BY  
      id asc
   LIMIT 
      0, 20

Since you are executing this query in Joomla you can try Tabulizer for Joomla (http://wwww.tabulizer.com) that can handle big data sets by using a data source cache (for your query results) and ajax loading, so only the first page of your table is fetched initially and rest of the data only when needed. Of course, the query needs to execute at least once for the cache to get populated, so you have to either improve it further or increase the available system resources (PHP memory and max execution time). This is most likely why it fails on the server and not on the local server, as most shared hosting environments have a max execution time for your PHP script 30 seconds.