I agree with the others that it would be imprudent to say something overtly negative about Bob. Though you might be able to get the client to realize by asking "innocent" sounding questions "Why did you and Bob decide to skip XXX?" "Is there room in the budget for rebuilding XYZ because we went did ABC?" etc.
If you can get this over quickly, you might suck it up and do that. But if this is a long term project, I think I would keep going to Bob with project stalling questions that he can't answer. He wanted to be in charge and the client agreed to that - let them rue the day. I would force him to make every decision and I would not give him a free web development education in the process.
If you believe Bob's decisions are putting the project in jeopardy you might say something to the client (or Bob) like:
"I understand I work for Bob on this project, but as a professional, I cannot, in good conscience, proceed per current direction. You are a very important client to me and your success is crucial. As a business owner myself, I also have a reputation for competence that I've worked many years to build. I cannot put my name and reputation behind the current design. eCommerce is very complex. There are laws and security issues... XYZ could happen...(blah blah blah say something to scare them straight here). The last thing I want to do is become one more problem to you, but I am extremely concerned about this and feel an ethical obligation to bring it to your attention."
On a side note:
The situation has changed. You had a direct client and now suddenly you are a sub contractor working for less money for Bob who doesn't know what he's doing. The message your client is getting is that you were over charging them in the past and you're desperate enough for work to lower your rates and give up your authority.
I don't know the details but I wonder if the fact that you accepted this project as Bob's contractor for less money than you normally charge lowers your value, and the value/importance of the work, in your client's eyes. You say the money doesn't matter, but I think it does. Maybe not to you personally, but it may affect how your client perceives you, or reveal how they saw you all along. Maybe something to think about...
I have learned that yes, it's good to be accommodating, but there is a line. I would never (now that I'm older and wiser) let a client turn me into a sub contractor for someone less competent than me and pay me less than they always have. You are where you are on this project but at the very least you can prepare yourself for how to handle things should this type of situation arise in the future, especially with this client.