GoObject.Remove() is responsible for removing the object from its parent group (if any) or from the layer that it is in (if any).
It isn't a user action, so there's no GoView event. Think of it like changing the Position of the object, or setting the Brush of a shape. You're just making a programmatic change, and the only event is a GoDocument.Changed event, if the object belongs to a document.
You can call GoView.DeleteSelection if you want all the GoView events that go with the user's delete action. But if you are just updating a GoDocument to correspond to changes in your model, I would think you would not want to get any events anyway.
You probably want to set GoPort.ClearsLinksWhenRemoved to false for every GoPort in your application. That way when a node is removed, no links are automatically removed -- your code to update the document from the model should be responsible for removing links from the document.
You might be interested in the UpdateDemo sample, which demonstrates updating a document upon changes to a model, and updating a model upon changes to a document. It also handles undo/redo changes. All updates happen at the end of transactions.