Here's a widget package I'm working on that uses a number of the Cordova plugins to achieve native features in a Mendix app:
The widget package contains the following:
While the documentation is still severely lacking, the widgets and source code should give you an idea about how you call/use Cordova plugins within a Mendix app.
Short answer: Yes
Long answer: Yes, you can
See the push notification widget:
https://github.com/mendix/MxPushNotifications
For an example of how you can use a cordova plugin widget with data from Mendix.
The documentation also gives you a good idea how you can include these plugins into your Mendix phonegap buiild: