WoW64 (Windows-on-Windows 64-bit) is a subsystem of Windows allowing you to launch 32-bit applications on all the 64-bit Windows versions. Launching of obsolete 16-bit applications on 64-bit Windows systems is impossible.
Wow64 subsystem emulates 32-bit environment with the help of an additional layer between a 32-bit application and 64-bit Windows API. In some places this layer is rather thin and in others it is not. For an average program presence of this layer will cause performance loss of about 2%. For some programs it can be greater. 2% is not much but you should take into account that 32-bit applications operate much slower under a 64-bit version of Windows operation system than under a 32-bit one.
Compilation of 64-bit code does not only exclude the necessity of WoW64 but also provides an additional performance gain. It is explained by architectural alterations within the microprocessor such as increase of the number of common-purpose registers. For an average program you can expect a 5-15% performance gain after simple recompilation of the program.
An additional performance gain can be achieved when using 64-bit data types. Viva64 static code analyzer can help you here. Although its main purpose is searching errors in 64-bit code, still you can increase a program's operation rate following its recommendations.