Mine didn't. I have no chapter breaks in my novel and my agent seems fine with it. I do have POV breaks that are marked, and those vary in length, I also have the book broken into three large parts (part I, etc.).
I think agents are open to all sorts of structure. It's one of those things that I don't think you have to worry about. If your story/writing/etc., is good enough, then even if an agent doesn't love the lack of chapter breaks, they will probably just suggest you change it down the line and you can hash it out with them.
Also, Cormac McCarthy's The Road (among many other great books) has no chapter breaks - and that won a Pulitzer...so I think you're in okay company.