Reddit has the true numbers. I'm sure 90% of people use the native Reddit app which is why they decided shutting down 3rd party apps wasn't a big deal.
I think why people are making it a big deal is because the 10% that used 3rd party apps were the most active users. A casual lurker probably didn't care about the features of the app they used. The very active users, and mods, likely used the 3rd party apps because of the superior design and features.
Time will tell whether this just upset a vocal minority or if it upset a core group of content creators and moderators.