SELECT nomenclature_types.nomenclature_type_key, count( DISTINCT(nomenclature.nomenclature_key) ) AS count
FROM nomenclature
LEFT JOIN nomenclature_types  USING(nomenclature_type_key)
WHERE
 `nomenclature`.`delete`!=1 AND
`nomenclature`.`use_in_eshop`=1
GROUP BY nomenclature_types.nomenclature_type_key\G

mysql> EXPLAIN SELECT nomenclature_types.nomenclature_type_key, count( DISTINCT(nomenclature.nomenclature_key) ) AS count FROM nomenclature LEFT JOIN nomenclature_types  USING(nomenclature_type_key) WHERE `nomenclature`.`use_in_eshop`=1 AND  `nomenclature`.`delete`=0  GROUP BY nomenclature_types.nomenclature_type_key;
+----+-------------+--------------------+------------+------+-----------------------+-----------------------+---------+-----------------------------------------------+-------+----------+----------------------------------------------+
| id | select_type | table              | partitions | type | possible_keys         | key                   | key_len | ref                                           | rows  | filtered | Extra                                        |
+----+-------------+--------------------+------------+------+-----------------------+-----------------------+---------+-----------------------------------------------+-------+----------+----------------------------------------------+
|  1 | SIMPLE      | nomenclature       | NULL       | ref  | delete,use_in_eshop   | delete                | 1       | const                                         | 30045 |    50.00 | Using where; Using temporary; Using filesort |
|  1 | SIMPLE      | nomenclature_types | NULL       | ref  | nomenclature_type_key | nomenclature_type_key | 38      | new_system.nomenclature.nomenclature_type_key |     1 |   100.00 | Using index                                  |
+----+-------------+--------------------+------------+------+-----------------------+-----------------------+---------+-----------------------------------------------+-------+----------+----------------------------------------------+
2 rows in set, 1 warning (0.00 sec)