If you need to get to market, then it could well be a win for both. If you then have significant traction and resources and still think 90% is good enough, well then, that's your risk to take as a business. Personally I feel that 90% is only good enough to get you started and there is a tipping point where user experience necessitates quality over business optimisations (shortcuts).
If cost of developing app is halved, many more apps will be built. The choice is often not between "expensive native app" and "cheap hybrid app", it's between "why is it so expensive? but I can afford this (hybrid app)" and "no way that's too expensive (native app)".
In theory, this might be true. In practice, I find that it is just an excuse to cut corners and ignore the problems.
I recently had to help somebody with their public library and a particularly magazine publisher for digital issues. They require a web app to read the issues. They were trying to use their Mac, but the site refused to load. The public library staff had no clue why it didn't work ("well, it works for us", and their attempts to contact the publisher was your stereotypical tech support horror story.) Long story short, their website doesn't work on all browsers. They implicitly know that it doesn't work in Safari because they apparently wrote a native app just for iOS. However, they have no native app for Mac and never bothered to fix their website.
But is it better to have more apps, if most of those apps work like shit? Wouldn't it be better to have fewer apps, (although I reject the premise that it would happen) but higher quality apps?
I don't think the tools we use impact the user experience that much, certainly not as much as the designs we use or the UX choices we make. If a hybrid app has a bad user experience it'd probably still be a bad experience if it'd have been built as a native app instead.
The article calls out scrollbar hijacking. That is a very example of the tools screwing up the user experience.
You generally don't have those problems in native. Apple in particular designs their APIs to steer you in the right direction and make it painful for you to do something that goes against their UX guidelines.
