Web apps can ask for your location or microphone the same way native apps can. Just reject it, there’s nothing that says you have to accept on either platform, so to say that’s a negative for native apps is odd.
The biggest downside of native apps is you can’t customize them with extensions or user styles like you can with websites.
I want native programs on my PC, and fewer apps on my phone.
I get all my apps from F-Droid. If I need to use Steam chat or view the menu at Taco Bell, mobile website it is. I am not gonna put their proprietary software on my phone. This also brings up another interesting difference. There is no desktop program for Taco Bell, that would be super weird. I think other comments already addressed that, but a lot of mobile apps are basically just the website.
A game like Luanti or some sort of Tetris is something I'd want native in both places (desktop and mobile). Games in browsers are a mess.