Yes, if you use Model.removeNodeData, the links will remain. See Model | GoJS API. Before removing, you could get the list of connected links and call Model.removeLinkData, but it may be easier to just call Diagram.remove if you want to remove everything together.
Here’s an item in the future version 2.0 change log:
Improved Model.updateTargetBindings and Part.updateTargetBindings to update Panels that have Panel.itemArray data bound if the contents of the Array have changed. In version 1, the reference to the Array had to have changed – the Panel.itemArray had to have been replaced. In version 2, the Panel.itemArray property setter checks to see if all of the Array items have corresponding Panels and that all child Panels correspond to Array items (i.e. Panel.data refers to the Array item), even if the new property value is a reference to the same Array that it had been before.