Currently, when asking Siri to call or message a friend, it will default to Phone or iMessage. If you want to use another service you have to specifically state that.
When the software refresh kicks in, Siri will default to the apps that people use frequently to communicate with their contacts. For example, if an iPhone user always messages another person via WhatsApp, Siri will automatically launch WhatsApp, rather than iMessage. It will decide which service to use based on interactions with specific contacts. Developers will need to enable the new Siri functionality in their apps. This will be expanded later to phone apps for calls as well.