If I have my game working on the Web, where people can play it without having to trust me, why would I want to replace it with a native desktop version where people do have to trust me to play it?
I know you're asking this question from an extraordinarily narrow point of view, but it isn't hard to see that doing this is really quite common and in demand.
Why do people use an HN app? I never knew they existed because, to me, the website is almost perfect.
There is no general answer other than "choice," and given a choice, there will almost never be an option everyone agrees on.
One of the laziest apps I ever saw was a MOTD that literally only had 365 quotes that occasionally got updated. Is that a real app? It's not even a real web app. To someone, it's the bee's knees I guess. Not I. But kudos to whomever made coin on such a thing. I thought it would have been brilliantly underhanded to write a horoscope app that way.
I think the answer is too often, “so we can control and milk our users more easily.”
The Reddit website doesn’t have to be garbage.
I think the famous vampire survivor game did this. FNF which is another game went viral with its web version and they're now working on a full release.