<body><![CDATA[]]></body>
or
<body></body>
Is there a difference or disadvantage for each? Do I need to do anything while parsing the XML? What do you prefer?
As far as the XML parser goes, there is NO difference. If you want to force CDATA to be generated during XSLT output, there is an option (cdata-section-elements) that can be used to allow some elements to output CDATA.