Unfortunately, yEd does not support decorations for a set of links (or rather edges in graph terminology). The best you can do is to simulate a link aggregation by creating an unconnected elliptical node with transparent/no fill color and move that unconnected ellipse over the edges you want to mark as aggregated:
Sample GraphML
You can use "Tools" -> Route Parallel Edges" to create parallel edge paths for multiple edges between the same source and target node(s).
