3D circuits would be denser (shorter propagation distances) than a planar circuit. In fact "computronium" is sort of an idea about how dense you can conceptually make computation.

You just can't really cool it that well with current technologies. Microfluidics are the current magic wand that everyone wishes existed but it's a ways away yet.

Signal propagation latency is only a problem if both end points need to be fully synchronous, which they don't have to be if they're independent units. Even the cores within single-chip multi-core CPUs aren't synchronous to each other, as far as I know.