Yes, that is possible. There are even two ways to realize sub-diagrams.
1. Use groups and folders. The easiest way to do that is
a.) creating the sub-diagram first
b.) selecting all nodes that belong to the sub-diagram
c.) using CTRL+G to group the selected nodes
d.) closing the grou[p nodes by clicking the nodes "-" icon.
The advantage of this approach is the fact that all information is contained in one file.
2. Use URLs to reference sub-diagrams. Create several GraphML files. Open the main diagram, select a node that should reference a sub-diagram. Find property "URL" in the properties table in yEd's lower right corner. Enter the relative path from the GraphML file of the main diagram to the GraphML file of the sub-diagram. To navigate from the main diagram to a sub-diagram, select the corresponding node in the main diagram and type F8.