Some lines of Atoms since mid-2010 or so have supported x86_64. The Sxxxx "server" atoms released at the end of 2012 are all 64-bit-enabled, for example, although they can still only take 8GB of RAM: http://ark.intel.com/products/series/71265
I agree that this is mainly interesting if you're I/O-limited. Most benchmarks show a "regular" recent-gen Intel CPU performing around 5x-10x the Atom, so if you're CPU-limited, even a low-end VPS that gives you an average of 1/4 share of a core will probably outperform sole tenancy on an Atom core. But a high-contention VPS in most cases will give you much worse I/O performance. Also, the storage space and bandwidth quota here are much better than with a comparably priced VPS.