There are no amd64 NanoBSD builds (yet, probably not for 2.0). The NanoBSD builds have their own set of features and limitations. They aren't right for everyone.
The major differences are:
NanoBSD only outputs to serial console (though there may be a VGA variant before 2.0 release)
NanoBSD keeps the media read only except for discrete write operations. (This makes it unusable for many packages)
NanoBSD has two main OS slices, and one separate configuration slice. Upgrade operations overwrite the currently unused "alternate" slice, and then boot from that.
NanoBSD has no installer, it can only be imaged to a disk and run directly.
NanoBSD only comes in 512MB, 1GB, 2GB, and 4GB sizes, so using it on HDDs would waste quite a lot of space. Using variable sizes is a non-trivial task.
The OS itself is basically the same between the two variants, though there are some kernel differences (a few drivers are left out, like certain SCSI drivers and RAID controllers).