On the server in the run the Workbench configuration manager as administrator and select the Alias Tab

Select the database in question and then click the Workbench button

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Uncheck the checkbox Alias visible in Workbench client

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Click OK to close the dialogue, bear in mind if you have IVPro you'll have hide the alias in there too. 

Click the IVPro button and uncheck the Show proactive alias and Show view-only alias boxes on the respective tabs, then click ok  to return to the Alias tab.

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 and then click Apply back on the Alias tab and say Yes to restart services.

You'll have to do this on each database that you want to hide.