I wondered the same thing when submitting a Cordova app to Apple, which is about 2% wrapping and 98% web site. Just this morning it got through the review process with no problems, so... data point!
That said, we did take pains beforehand to make the "web site" behave like an app: responsive, (mostly) single page, swipe support, and tested across all devices.
My team just got a Cordova app through the apple review process as of yesterday. So, data point #2! I think as long as you try to adhere to Apple's app review guidelines it doesn't matter if you used Cordova or developed natively
That said, we did take pains beforehand to make the "web site" behave like an app: responsive, (mostly) single page, swipe support, and tested across all devices.