SELECT 
  lnk.link_id, 
  lnk.usergroup_id, 
  lnk.status 
FROM 
  cscart_usergroup_links as lnk 
  INNER JOIN cscart_usergroups ON cscart_usergroups.usergroup_id = lnk.usergroup_id 
  AND cscart_usergroups.status != 'D' 
WHERE 
  lnk.user_id = 0 
  AND lnk.status IN ('A')

Query time 0.00047

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "0.38"
    },
    "nested_loop": [
      {
        "table": {
          "table_name": "lnk",
          "access_type": "ref",
          "possible_keys": [
            "user_id"
          ],
          "key": "user_id",
          "used_key_parts": [
            "user_id"
          ],
          "key_length": "3",
          "ref": [
            "const"
          ],
          "rows_examined_per_scan": 1,
          "rows_produced_per_join": 0,
          "filtered": "10.00",
          "cost_info": {
            "read_cost": "0.25",
            "eval_cost": "0.01",
            "prefix_cost": "0.35",
            "data_read_per_join": "1"
          },
          "used_columns": [
            "link_id",
            "user_id",
            "usergroup_id",
            "status"
          ],
          "attached_condition": "(`dev_yourmart_co_bw`.`lnk`.`status` = 'A')"
        }
      },
      {
        "table": {
          "table_name": "cscart_usergroups",
          "access_type": "eq_ref",
          "possible_keys": [
            "PRIMARY",
            "c_status",
            "status"
          ],
          "key": "PRIMARY",
          "used_key_parts": [
            "usergroup_id"
          ],
          "key_length": "3",
          "ref": [
            "dev_yourmart_co_bw.lnk.usergroup_id"
          ],
          "rows_examined_per_scan": 1,
          "rows_produced_per_join": 0,
          "filtered": "100.00",
          "cost_info": {
            "read_cost": "0.03",
            "eval_cost": "0.01",
            "prefix_cost": "0.39",
            "data_read_per_join": "1"
          },
          "used_columns": [
            "usergroup_id",
            "status"
          ],
          "attached_condition": "(`dev_yourmart_co_bw`.`cscart_usergroups`.`status` <> 'D')"
        }
      }
    ]
  }
}