Yep. Native applications are much faster, more reliable (can't change underneath you unless you let them), incomparibly more private, and generally longer lasting.
Using the web for applications forces you into behavior and situations you wouldn't accept otherwise. Web sites are best made of web pages. Not executable code. And there are still more web sites made out of web pages out there than corporate web apps. The web is huge and there's a lot beyond the top 100 web apps everyone use.
Turning off JS auto-execution helps one avoid falling into those traps as well as avoiding fingerprinting in general. And the vast majority of the non-commercial web still works just fine.
Given how websites are built these days, if you just turn javascript off, half of them, if not more, will become unusable.