Do they offer an affiliate program for promoting their cart that you could monetize?

Ultimately if it is hosting and managing you aim toward then your own code is what should be on the back end so there are no issues.

As licensing goes, you might be able to arrange volume licensing that applies only to sites hosted by you and operating under your control (in some sense), such as a central check out that all your clients' customers final orders are processed through.

It would after all be only one license in play (at the check out, anyway) and perhaps they mightn't see it as distribution if it all funnels to one place in the end. It would be easy enough to account for the activity in terms of numbers and client front-ends.

If you really like the shopping cart, then throw some weight behind it and start the ball rolling. Talk to the folks who own it and fire them up. They might come back to you with an even better proposition than you anticipated or asked for.

In today's business climate it will be the ones who work together that will thrive.