In your wsdl, you have a complexType with 2 levels
<s:element name="GetClientesNif">
<s:complexType>
<s:sequence>
<s:element minOccurs="0" maxOccurs="1" name="empresa" type="s:string"/>
<s:element minOccurs="0" maxOccurs="1" name="password" type="s:string"/>
<s:element minOccurs="0" maxOccurs="1" name="nif" type="s:string"/>
</s:sequence>
</s:complexType>
</s:element>
That's why you need to send a request with a 2 levels array :
Try with this :
$myArray[] = array(
'empresa' => '*****',
'password' => '******',
'nif' => '*******',
);
$clientVAT = $c->call('GetClientesNif', $myArray);