Try creating a nil value SoapParam. Something like this...
$nilDependentsParam = new SoapParam(null, "Dependents");
Now, when you make your SOAP call, include the SoapParam in the array that you will send. Something like this...
$theResponse = $client->__soapCall("theMethodIAmCalling",
array($nilDependentsParam, $otherDataIAmSending)
);
If you check the XML that is sent you will see it is set to:
<Dependents xsi:nil="true"/>
With any sort of luck that should be all you need to do.