Well, you could edit your GraphML file to convert the description to a custom property, then use "Edit" -> "Properties Mapper" to set the text of your nodes to the information in the description-turned-custom-property.
To do so, open your GraphML file in a text editor and locate the line
<key attr.name="description" attr.type="string" for="node" id="dXXX"/>
where XXX is some number. Change this line to
<key attr.name="mydescription" attr.type="string" for="node" id="dXXX">
and save as new file. Now open the modified file in yEd, go to "Edit" -> "Properties Mapper", click the green "+" icon and choose "New Configuration for Nodes". Finally click "Ok". The information from Data-description should now have replaced the "useless" 1, 2,... texts.
For future uses consider putting additional information either in the text box right away or into custom properties that may be used to automatically generate tooltips (Data-description) and texts as needed.