IOS – Can each application have a separate merchant account

Each client will need to have an enterprise account. If they want to, they can share their distribution key with you, and you can build an app for distribution within their organization. If the number of clients isn't large, this shouldn't be a big deal -- you can just set up a different target for each client, and then use an aggregate target to build them all at the same time.

Over the air distribution is definitely possible. One way is by making the app available for download on a restricted access web server; another is to install it directly on any managed devices using mobile device management.

I believe most of your questions are answered in the enterprise program agreement. Give that a careful reading if you haven't already. Questions about how to interpret a legal agreement are probably off topic for this forum, but I think you'll find the agreement to be fairly easy to understand as legal documents go.

Update: Another option that's been available for a while now (though possibly not when I wrote the answer above) is custom B2B distribution. You can offer your apps for sale through Apple's Volume Purchase Program directly to your clients. That is, your clients would purchase through the Volume Purchase Program (essentially the App Store, but multiple licenses) and then distribute your app via Mobile Device Management or redemption codes. The down side of this plan is that Apple would take the usual App Store cut of the selling price.

The rules of iTunes connect are only really available when you sign in to the service, and agree to the terms. I am not currently a developer so I don't know even if the details are protected by an NDA.

I don't have a link to a good press article covering the current state of affairs, but my understanding and gross oversimplification of the rules are:

• It's OK to enable extra content if the iOS app does nothing to link to, process, enroll or advertise the paid portion of the service or app.
• It's always OK to handle purchases through in-app purchase where Apple will take their cut of the sale in return for providing the accounting, customer service, billing, returns, server hardware, software and bandwidth for distribution of your app and the handling of the paid content sales. It's probably very not OK to sell in the app and not use Apple for the payment.
• Newsstand apps are different and I'll let someone who knows edit in how a subscription might be different than a one time sale, but I would be surprised if it was overall different than the normal in-app purchase policy.

If your work for your client is to advise them, you'll really want to just spend the $99 and join and have your team participate in the developer program NDA / restricted chats and or just read the terms of iTunes Connect. If not, it's their problem and make sure your contract with them is clear as to under whom all responsibility of knowing and adhering to the Terms and Conditions fall.