Does mysqldump export indices, by default?
No, it does not export indexes. Indexes are rebuilt upon loading the mysqldump back into mysql. The options you found "--disable-keys" cause the the mysqldump to write something like this before the table's load via INSERTs:

DROP TABLE IF EXISTS `tblAccountLinks`;
SET @saved_cs_client     = @@character_set_client;
SET character_set_client = utf8;
CREATE TABLE `tblAccountLinks` (
  `ID` int(11) NOT NULL auto_increment,
  `FirmNo` varchar(10) NOT NULL,
  `CustomerNo` varchar(20) NOT NULL,
  `AccountNo` varchar(20) NOT NULL,
  `LinkType` smallint(6) NOT NULL,
  `AccessLevel` smallint(6) NOT NULL,
  `Status` smallint(6) NOT NULL,
  `CreatedOn` datetime NOT NULL,
  PRIMARY KEY  (`ID`)
) ENGINE=InnoDB AUTO_INCREMENT=27023 DEFAULT CHARSET=latin1;
SET character_set_client = @saved_cs_client;

--
-- Dumping data for table `tblAccountLinks`
--

LOCK TABLES `tblAccountLinks` WRITE;
/*!40000 ALTER TABLE `tblAccountLinks` DISABLE KEYS */;
INSERT INTO `tblAccountLinks` VALUES (1,'F0001','C001','T00000001',1,2,1,'2008-06-30 07:55:43'),(2,'
F0001','C001','T00000002',2,2,1,'2008-06-30 07:55:43'),(3,'F0001','C002','27601012',1,2,1,'2008-06-3 ...


The line after LOCK TABLES is

/*!40000 ALTER TABLE `tblAccountLinks` DISABLE KEYS */;


This is what the --disable-keys option embeds in the mysqldump.

Also, this is embedded after all the INSERTs are done

/*!40000 ALTER TABLE `tblAccountLinks` ENABLE KEYS */;
UNLOCK TABLES;


CAVEAT #1


  DISABLE KEYS and ENABLE KEYS were
  implemented to disable the reloading
  of nonunique indexes while a table is
  being reloaded. Primary Keys and
  Unique Keys are not disabled. They are
  loaded at the same moment the INSERTs
  are being. Once you ENABLE KEYS, the
  nonunique indexes are rebuilt via
  sorting (or using the MyISAM key cache is there isn't
  enough available memory)
  
  Unfortunately, DISABLE KEYS and ENABLE
  KEYS only work for MyISAM tables, not
  InnoDB.


CAVEAT #2

You do not have to --disable-keys. You could disable DISABLE KEYS (no pun intended) them with --skip-disable-keys:

  -K, --disable-keys  '/*!40000 ALTER TABLE tb_name DISABLE KEYS */; and
                      '/*!40000 ALTER TABLE tb_name ENABLE KEYS */; will be put
                      in the output.
                      (Defaults to on; use --skip-disable-keys to disable.)


This could result in a slower load and a potential lopsiding of the index pages for nonunique indexes.

CAVEAT #3

You can dump the actual InnoDB tablespaces (MySQL 5.5.12)

  -Y, --all-tablespaces 
                      Dump all the tablespaces.
  -y, --no-tablespaces 
                      Do not dump any tablespace information.