Where I live, most all diners are all their phones throughout their meals, so I don't think it's unusual.
The best advice I can give is:
-Don't be so worried about being rude. You have a job to do and you are better off being slightly rude than not having the pertinent details.
-I tell my guests that I will be on the phone for a good portion of the meal. That lets them off the hook so that they can be texting or using FaceBook, and we just look like many of the other diners in that case. If you are taking notes and your guest is just sitting there...that's when it looks the most rude.
-Sit with you back to the wall at any restaurant and be sure you guest knows to give you that seat. You can see the server coming & going that way and not be taking notes that they can see.
-Develop a shorthand for your notes. Most of my notes are VERY short, and indecipherable to others ("20 m10sbg c&w" means to me, "At 7:20 PM, a male, 5'10", short black hair with glasses, cleared and wiped down the table."
-Try to practice remembering 2, then 3, then 4 interactions before jotting them in your notes. I usually makes the notes when I have 3 or 4 timings to notate.
-Put your guest in charge of names. You work on the timings and have your guest collect names if the staff wear name tags. If not, leave it to them to ask the name in conversation, in exchange for their free meal. It will make you less suspicious...Your the one on the phone and they're the one looking at everyone's name tag. Have them text you the staff names and that will also help with timings.