Very easy. I've rented from them many times.
You go to the Hertz/Toyota desk and they are ready with the paperwork and car keys. You'll get what you reserve, so expect no upgrades or Gold service. After all, it's not really a Hertz, but rather Toyota-Rent-A-Car. You'll need your passport and IDP; they'll make a photocopy of it; they will always ask your permission first. For some reason they never want to see my actual driver's license, just the IDP.
If you don't have an ETC card, you can rent one too. Trust me you want to rent one. There is no fee for renting, but you'll be charged for whatever tolls you incur after you return the car. They only have a limited supply of them, so they might run out. They may or may not offer this straight off, so you should ask them for one if they don't offer straight off.
They tell you where you can fuel up the car before returning the car and the navigation runs off phone numbers so everything is easy to use. Although the pick up is at the airport, the actual rental location is off airport location. So don't expect to swap cars; you take what you get. After returning to the off airport location, they will give you free private drive back to the terminal.
All the cars have built-in sat nav, but the only issue I have is unless you call in you can never be sure to get one with English navigation. Even if you do call in you may still end up with one with only Japanese. So be prepared for that.
Otherwise it's all very easy. They're very efficient and nice people. Expect no trouble or rudeness, but they also stick to the rules.
Anyways the only car I find you can't rent on Hertz is the Toyota 86, which you can only rent directly if you call Toyota. Their English hotline is very good you can ask for a English navigation in which it's guaranteed. If you reserve on the Japanese site you can choose other options including prepaying to get a 5% discount. My GF helped me with getting through the Japanese site.
Happy driving in Japan. I'm picking up an 86 this weekend in Nagoya (for the GP).