The issues are quite noticeable for someone that isn't heavily invested in web apps. Most of HN is - and that's why they prefer to ignore them.
But let's look at the market... Have web apps displaced desktop apps? No. Have they displaced mobile apps (as per HN mantra 90% of iPhone apps could be web apps)? Not even close.
Now why is this? It's because web apps offer a significantly poorer user experience across the board.
* with all the progress that's been made in performance, web apps are slower than native apps and will continue to be. There is only so much that you can offload from JS.
* web-apps don't have access to the platform's entire range of graphics capabilities, including standard widgets, animations and so on.
* web apps don't have access to special platform functionality such as GPS, sensors, camera, etc.
Furthermore, the biggest mobile players have all started to invest in native mobile apps to the detriment of web apps. Including Google. It's in their interest to lock-in users to their platform, even more so since Android became a major player.
These issues can be worked around eventually (maybe).
The core issues with web apps can't be worked around:
1. Web apps are using a text-transfer protocol with a pile of hacks on top to make it stateful. To this day engineers are still working on solving this problem (web sockets, web sql, etc). They can't solve it.
2. One does not own web apps, one merely rents them.