If your speaking to removing a custom property from the custom properties resource in the web console you can hide custom properties by using "edit" for the resource (not the custom properties) with in the view.
Then you can select which properties are viewable in the resource.
As a side note, properties that are not populated are not displayed.
I would have to agree with dnerdahl that the only way to hide them would be to remove the option from the resource in the node details page. Otherwise, in Edit Nodes, and Custom Property Editor you'll see all properties on all nodes.