And for years, it was our most requested feature, by far. We had instructions for how to pin the site to your home screen, and would explain to users how the website does everything an app can do. Still, constant requests for an app. Finally we relented and released one, and very quickly around half our mobile traffic moved to the app without us really trying to nudge people at all.
People just really like apps! I think it suits our mental model of different tools for different uses. We've also found that app users are much more engaged than website users, but of course much of that will be selection bias. Still, I can see how having your app on someone's home screen could provide a significant boost to retention, compared to a website they're liable to forget. For us now, that's the main benefit we see. Certainly don't use any additional data, though I won't argue that other companies don't.
This is it. I’ve worked on plenty of projects that have web/iOS/Android, and the reason for offering native apps has always been user demand. All of this “spy on the user” crap literally never even comes up in conversation. We don’t care at all. We care about native apps because users care about native apps.
It you’re talking about the intrusive stuff that gets in the way of you using the website, then the answer to this is pretty simple: they don’t. The sites that do that are comparatively rare. They just appear more numerous than they really are because it’s the really big sites like Reddit that do it. The norm is either a page on the site that tells you about the app, or the banner that appears at the top of a page.