Unfortunately, yEd's "Automatic Grouping" feature does not support grouping by properties.
If you do not have too many different property values, try using "Tools" -> "Select Elements" to select exactly those nodes with a given property value. Then use "Grouping" -> "Group" to create a common parent group for the selected nodes. Repeat "Select Elements" and "Group" for each distinct property value.
Unfortunately, a node may only belong to at most one group. The only way to give the impression of a node belonging to several groups is to assign the node to one of those groups and manually move the other group over or under said group. You will have to use (semi-) transparent fill colors for your groups for this approach to create the desired visual effect.