SELECT 
  products.company_id, 
  COUNT(DISTINCT products.product_id) as products_count 
FROM 
  cscart_products as products 
  LEFT JOIN cscart_product_descriptions as descr1 ON descr1.product_id = products.product_id 
  AND descr1.lang_code = 'ja' 
  LEFT JOIN cscart_product_prices as prices ON prices.product_id = products.product_id 
  AND prices.lower_limit = 1 
  LEFT JOIN cscart_companies AS companies ON companies.company_id = products.company_id 
  INNER JOIN cscart_products_categories as products_categories ON products_categories.product_id = products.product_id 
  INNER JOIN cscart_categories ON cscart_categories.category_id = products_categories.category_id 
  AND (
    cscart_categories.usergroup_ids = '' 
    OR FIND_IN_SET(
      0, cscart_categories.usergroup_ids
    ) 
    OR FIND_IN_SET(
      1, cscart_categories.usergroup_ids
    )
  ) 
  AND cscart_categories.status IN ('A', 'H') 
  LEFT JOIN cscart_product_review_prepared_data ON cscart_product_review_prepared_data.product_id = products.product_id 
  AND cscart_product_review_prepared_data.storefront_id = 0 
WHERE 
  1 = 1 
  AND companies.status = 'A' 
  AND products.status IN ('A') 
  AND (
    products.usergroup_ids = '' 
    OR FIND_IN_SET(0, products.usergroup_ids) 
    OR FIND_IN_SET(1, products.usergroup_ids)
  ) 
  AND products.status IN ('A') 
  AND prices.usergroup_id IN (0, 0, 1) 
  AND products.parent_product_id = 0 
  AND products.company_id IN (2, 1) 
GROUP BY 
  products.company_id

Query time 0.00216

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "products.company_id",
      "temporary_table": {
        "table": {
          "table_name": "cscart_categories",
          "access_type": "index",
          "possible_keys": ["PRIMARY", "c_status", "p_category_id"],
          "key": "p_category_id",
          "key_length": "773",
          "used_key_parts": ["category_id", "usergroup_ids", "status"],
          "rows": 83,
          "filtered": 100,
          "attached_condition": "(cscart_categories.usergroup_ids = '' or find_in_set(0,cscart_categories.usergroup_ids) or find_in_set(1,cscart_categories.usergroup_ids)) and cscart_categories.`status` in ('A','H')",
          "using_index": true
        },
        "table": {
          "table_name": "products_categories",
          "access_type": "ref",
          "possible_keys": ["PRIMARY", "pt"],
          "key": "PRIMARY",
          "key_length": "3",
          "used_key_parts": ["category_id"],
          "ref": ["smscrm_edev.cscart_categories.category_id"],
          "rows": 2,
          "filtered": 100,
          "using_index": true
        },
        "table": {
          "table_name": "products",
          "access_type": "eq_ref",
          "possible_keys": ["PRIMARY", "status", "idx_parent_product_id"],
          "key": "PRIMARY",
          "key_length": "3",
          "used_key_parts": ["product_id"],
          "ref": ["smscrm_edev.products_categories.product_id"],
          "rows": 1,
          "filtered": 95.97764587,
          "attached_condition": "products.parent_product_id = 0 and products.`status` = 'A' and (products.usergroup_ids = '' or find_in_set(0,products.usergroup_ids) or find_in_set(1,products.usergroup_ids)) and products.company_id in (2,1)"
        },
        "table": {
          "table_name": "prices",
          "access_type": "ref",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "usergroup",
          "key_length": "3",
          "used_key_parts": ["product_id"],
          "ref": ["smscrm_edev.products_categories.product_id"],
          "rows": 2,
          "filtered": 92.49011993,
          "attached_condition": "prices.lower_limit = 1 and prices.usergroup_id in (0,0,1)",
          "using_index": true
        },
        "block-nl-join": {
          "table": {
            "table_name": "companies",
            "access_type": "ALL",
            "possible_keys": ["PRIMARY"],
            "rows": 2,
            "filtered": 100,
            "attached_condition": "companies.`status` = 'A'"
          },
          "buffer_type": "flat",
          "buffer_size": "873Kb",
          "join_type": "BNL",
          "attached_condition": "companies.company_id = products.company_id"
        }
      }
    }
  }
}