It's been a couple years, but I seem to remember having to take a short shuttle ride to the rental cars.
I don't think any of the HI locations have Emerald Isle. I'm Exec Elite so I get upgrades automatically. Probably not with regular Emerald Club. But rental cars are cheap on the islands, you can probably deal with them for an upgrade.
Watch out for the traffic. Last time I went there it took me almost 45 minutes to drive the 5 miles from the airport to Kona.
Have fun.
Matt