I mostly use the reader, but do make sure I scan with my phone every 8 hours.
I find the reader much more convenient to use for a couple reasons:
1. its much smaller than my phone - almost a third the size of a OnePlus3 which means its a lot less obvious to every one else when I'm using it.
2. it's nfc sensor is obviously a lot more powerful than my phones, the reader can read the sensor from 4-5cm away - it'll read it through a t-shirt, thick fleece and coat, whereas my phone needs to be very close and can be very awkward to actually get it to read - maybe my phone nfc sensor is just truly rubbish I don't know.
3. I can mute the reader when it scans so it only vibrates, the phone app appears to have no such setting so the whole office can hear it when I use it in the office unless my phone is set to vibrate only.
I still make sure I scan it with the phone though cos the phone has a much bigger screen so when showing my DN whats been going on, its a lot easier to see and also navigate using the app