Ioinc Deploy only updates the content of your app, what you locally have in www. Native code that is generated e.g. with values from config.xml can not be updated - that has to be uploaded to the app stores as usual.
So even after a Live Update with Ionic Deploy the actual app version is the same. Only the content inside has changed. You might want to include another version number for the “app content” that is saved in your Ionic app itself.