Does that involve shipping a native wrapper for your web app?

If so, you have the extra cost, effort and bureaucracy of building and deploying to all the different app stores. Apple's App Store and Google Play each have various annoyances and limitations, and depending on your market there are plenty of other stores you might need to be in.

Sometimes you do need a native or native-feeling app, in which case a native wrapper for JS probably is a good idea, other times you want something lightweight that works everywhere with no deployment headaches.