It's not the bus speed in most cases (which is usually 533MHz on these ITX boards - comparable to an old Core2). The Atom has plenty of memory bandwidth for most applications. Besides, MAME isn't exactly hurting for memory bandwidth on anything resembling a modern PC.
The issue is that the Atom's CPU core is VERY simple. It's strictly in-order, and I believe it can only issue one instruction per clock per thread. While these are dual core and hyperthreaded, this means that it can only attain an IPC of, at best, 4, and that's if you've got 4 threads running that just happen to use completely different parts of the two cores. A Pentium 3 can pull that off on a single core without hyperthreading, and it supports out-of-order execution.
Figure a 1.6GHz Atom is about like having a 1.6GHz Pentium (original) with modern SSE instructions. While it would be 16 times faster than a 100MHz Pentium of yore, and you've got two of 'em (2 cores) a 1.6GHz Core i7 will kick the everloving butt out of it, even though it's got the same clock speed, since it can do so much more in one clock cycle.
Some of the modern ARMs they're throwing in cell phones and tablets are actually capable of more advanced instruction scheduling (minimal out-of-order issue, and they're superscalar) than these Atoms, and their starting to get the clock speeds comparable. And they do it all while drawing about 1/6th the power of what an Atom solution does and at similar price. Intel just has no idea how to make a small, low cost, low power CPU. They're great on the high end, but they just have no experience on the low end.
Note that you can get mini-ITX boards that take "conventional" CPUs and offer conventional CPU sockets. You can't use a really power hungry CPU on them, since there's no way to heatsink the 80W+ monsters, but you can usually put a dual core ~2GHz Phenom II or similar on them. That'll kick the crap out of any Atom based board in the same formfactor, albeit at 3-4x the cost and about 5-6x the power consumption.