It's either plain text or HTML, there are no other flavours. So either the only 'layout' you can maintain are the linefeeds, or you have to handle the entire HTML as a blob.
If you want anything fancier, maybe you can find a library to parse the HTML, but then you're left with the decision what format you want next; HTML to RTF maybe?
(And you would have to do RTF to HTML again if you also write back to EWS).
BTW I'm suprised you write "e.g. empty lines": the text does contain line feeds:
(Added 22-1-2014 in response to your comment:)
When I edit a mail in Outlook like this:
- Sample text starts -
Next line followed by 1 empty line
Next line followed by 2 empty lines
- Sample text ends -
and retrieve it with SOAPUI as text I get:
<t:Body BodyType="Text">- Sample text starts -
Next line followed by 1 empty line
Next line followed by 2 empty lines
- Sample text ends -</t:Body>
I suggest you take a good look at your code or that of the EWS Java API if linefeeds are disappearing.
SOAPUI is a nice tool to query your actual data, but you will have to learn how to construct the SOAP requests. I used Inside Microsoft® Exchange Server 2007 Web Services for that.