SELECT 
  a.shipping_id, 
  a.company_id, 
  a.min_weight, 
  a.max_weight, 
  a.position, 
  a.status, 
  a.tax_ids, 
  a.usergroup_ids, 
  b.shipping, 
  b.delivery_time, 
  c.company AS company_name, 
  storefront_id 
FROM 
  netting_shippings AS a 
  LEFT JOIN netting_shipping_descriptions AS b ON a.shipping_id = b.shipping_id 
  AND b.lang_code = 'en' 
  LEFT JOIN netting_companies AS c ON c.company_id = a.company_id 
  LEFT JOIN netting_storefronts_shippings AS storefronts_shippings ON storefronts_shippings.shipping_id = a.shipping_id 
WHERE 
  1 = 1 
  AND (
    a.company_id = 3 
    OR a.shipping_id IN (8, 11, 16, 13, 3, 14) 
    AND a.company_id IN (0, 3)
  ) 
  AND (
    storefronts_shippings.storefront_id IN (1) 
    OR storefronts_shippings.storefront_id IS NULL
  ) 
ORDER BY 
  a.position

Query time 0.00094

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "a.position",
      "temporary_table": {
        "nested_loop": [
          {
            "table": {
              "table_name": "a",
              "access_type": "ALL",
              "possible_keys": ["shipping_id"],
              "rows": 8,
              "filtered": 100,
              "attached_condition": "a.company_id = 3 or a.shipping_id in (8,11,16,13,3,14) and a.company_id in (0,3)"
            }
          },
          {
            "table": {
              "table_name": "b",
              "access_type": "eq_ref",
              "possible_keys": ["PRIMARY"],
              "key": "PRIMARY",
              "key_length": "9",
              "used_key_parts": ["shipping_id", "lang_code"],
              "ref": ["pucuda_cscart.a.shipping_id", "const"],
              "rows": 1,
              "filtered": 100,
              "attached_condition": "trigcond(b.lang_code = 'en')"
            }
          },
          {
            "table": {
              "table_name": "c",
              "access_type": "eq_ref",
              "possible_keys": ["PRIMARY"],
              "key": "PRIMARY",
              "key_length": "4",
              "used_key_parts": ["company_id"],
              "ref": ["pucuda_cscart.a.company_id"],
              "rows": 1,
              "filtered": 100
            }
          },
          {
            "block-nl-join": {
              "table": {
                "table_name": "storefronts_shippings",
                "access_type": "index",
                "key": "PRIMARY",
                "key_length": "8",
                "used_key_parts": ["storefront_id", "shipping_id"],
                "rows": 1,
                "filtered": 100,
                "using_index": true
              },
              "buffer_type": "flat",
              "buffer_size": "35Kb",
              "join_type": "BNL",
              "attached_condition": "trigcond(storefronts_shippings.storefront_id = 1 or storefronts_shippings.storefront_id is null) and trigcond(storefronts_shippings.shipping_id = a.shipping_id)"
            }
          }
        ]
      }
    }
  }
}

Result

shipping_id company_id min_weight max_weight position status tax_ids usergroup_ids shipping delivery_time company_name storefront_id
16 0 0.000 0.000 0 A 0,1,2,3 FedEx
8 0 0.000 70.000 0 A 0,1,2,3 USPS 2-5 business days
11 0 0.000 150.000 0 A 0,1,2,3 UPS 1
13 0 0.000 0.000 1 A 0 FedEx 1 day Freight
3 0 0.000 0.000 2 A 6 0,1,2,3 FedEx 2 day Frieght
14 0 0.000 0.000 3 A 0,1,2,3 FedEx 3Day Freight