SELECT 
  COUNT(*) 
FROM 
  cscart_storefronts AS storefronts 
  LEFT JOIN cscart_storefronts_companies AS companies ON storefronts.storefront_id = companies.storefront_id 
WHERE 
  1 = 1 
  AND (
    companies.company_id IN ('1')
  )

Query time 0.00057

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "companies",
      "access_type": "index",
      "possible_keys": ["PRIMARY", "idx_storefront_id"],
      "key": "PRIMARY",
      "key_length": "8",
      "used_key_parts": ["storefront_id", "company_id"],
      "rows": 2,
      "filtered": 100,
      "attached_condition": "companies.company_id = '1'",
      "using_index": true
    },
    "table": {
      "table_name": "storefronts",
      "access_type": "eq_ref",
      "possible_keys": ["PRIMARY"],
      "key": "PRIMARY",
      "key_length": "4",
      "used_key_parts": ["storefront_id"],
      "ref": ["orbit_cscart_orbit_cscart.companies.storefront_id"],
      "rows": 1,
      "filtered": 100,
      "using_index": true
    }
  }
}