Really hinders app use too, and devs must know it. I barely ever use the Facebook app on Windows 10, even though it's probably a better experience than the desktop site (for my SP3). I never use Baconit on desktop also, even though I have it installed and I browse Reddit a fair bit. I go through YouTube and Twitch's sites, despite both having really solid third party apps available.
On the Android phones I'm using right now it's a completely different story. Twitter links open in the app. Vine links open in the app. Imgur links open in the app. And honestly, especially when you're using touch, it's just a nicer experience. They even have a tablet mode that automatically sets itself when disconnected from a keyboard, so they could change the deep linked behaviour based on whether I'm in tablet mode or not. Tablet mode? Open the app. Desktop mode? Open in browser.
I understand trying to push everything to be through the web, but for some things it's just not as good, and lots of sites have better apps than mobile websites these days.