The Vuforia SDK allows you to remove targets from a Dataset, only if the targets have not been loaded from a Device Database.
This practically means that you can only remove User Defined Targets (UDT).
This can be achieved using the Dataset class methods.
JAVA (Android native):
myDataSet.destroy ( myUserDefinedTarget );
C++ (Android and iOS native):
myDataSet->destroy ( myUserDefinedTarget );
See also API reference:
myDataSet.Destroy( myUserDefinedTarget, true );
See also the API reference: https://developer.vuforia.com/resources/api/unity/class_data_set
Note that the Unity API - Destroy() method takes an additional boolean argument (true / false) to specify whether you want the gameObject associated to the target to be destroyed or not.