One vocal user of Coq under Cygwin found the 32-bit version to be faster than the 64-bit version, because of cache effects and the like. But I believe this user is moving to the 64-bit version anyway, because 32-bit Cygwin is being phased out and limits memory usage too much (2 Gb max per process? maybe even less).
The writing is on the wall. Everyone is dropping 32-bit x86 support. Good riddance.