What method do you suggest for prototyping asynchronous circuits?
The Theseus logic NCL has been mentioned, there was also Handshake systems (Philips spin off) as well as Fulcrum Microsystems and Caltech. There was a asynchronous ARM processor called Amulet as well. And SUN Microsystems had a processor design team for this as well for a clockless SPARC.

I would call these clockless designs to avoid the confusion between logic design like ripple counters and these types of circuits.  But in general either term is used.

DC (Design Compiler) from Synopsys as well Merlin from FTL systems also used to be available.

However, if you have a properly designed library of core cells this top level abstraction/description can become trivial. The core issue is that if you've designed a system that allows each cells to propagate forward a signal that says "result good" as well as propagating backwards "system available" the system self clocks and as such can be simply designed very much like software without concern for race conditions or timing for that matter.

So the tools used would be as simple as SPICE for cell level (transistor level) design and C for compiling into a set of primitives to be placed. For the life of me I can't find the C based tool (open source) that was used.

Look to people like Wesley Clark (He passed away recently) as well Ivan Sutherland and Karl Fant (mentioned elsewhere too).