When you enable duplicate detection and publish your duplicate detection rules, you will notice that when you try to create a duplicate in the CRM web application (or through Outlook client) you will get a pop-up indicating that you are trying to create a duplicate record. However, if the create/update request is sent via the web services to CRM (using the SDK) then by default, the duplicate record will be created without any warning.
The trick is that if you want to avoid creating duplicates when calling the CRM web services, you need to provide an optional parameter in the request which specifies that the server should check for duplicates before creating your record (by default the server will bypass duplicate detection). You must use a CreateRequest or UpdateRequest and provide the SuppressDuplicateDetection as “false”. Here is a sample for which my code will prevent creating duplicate accounts (note that I have already published a duplicate detection rule for accounts with the same name):