I realize that this is old, however for future reference it might help to state the solution here:
If you're referencing any existing object in a csv in order to update or delete it, you always have to specify which property (or properties) you are using to identify this object via the system_identity_properties entry.
In your case, the csv has to look like that:
With the command
./ImportExportCLI.exe export -usr <usr> -pwd <pwd> -con <url> -mt DeploymentTarget -format csv -fi <file>
your Target will be deleted.
Note 1: A good first step in any API/importExportCLI-action is to export the entities first.
Note 2: In case an object needs to be referenced by more than one property (a component can be referenced by system_name and system_application, as the name is not unique!), you have to seperate the system_identity_properties by #;#:
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