> I don't believe a website can upload your contact list

Requires an opt-in permission on native, for browsers with support, it would also be an opt-in permission

> upload a list of apps on the device

Not possible on iOS for a native or web app. Depends on a number of factors on Android.

> log your GPS location or record using your camera or microphone.

Possible for native and web apps, but only after explicit opt-in permission.

End result, no meaningful difference between native and web for any of your examples.

> I don't believe a website can upload your contact list, upload a list of apps on the device,

True AFAIK.

> log your GPS location or record using your camera or microphone. Is this no longer true?

Depends on what you mean. This is fully possible on many phones and only needs approval from the user.

Then again approval from the user seems to be becoming the standard in installed apps as well.

That said, I much prefer web pages for things that need cloud or apps/desktop applications that works offline for the rest.

You can let the website do all these things however they would have to ask for an extra permission to access these API just like the native apps have to ask for extra permissions to access these API.