WoW64 makes it possible to run 32 bit applications on 64 bit Windows. If the conversion from 32 bit instructions to 64 bit instructions can be made at runtime, why can't we convert the executable itself to 64 bit?
That is because WoW64 doesn't convert 32bit instructions to 64bit.
Your 32bit executable is run in 32 bit mode by switching your CPU to compatibility mode. There are some conversions inlined for API/driver calls, but most of the code is not converted.
*This is only true for the x86-64 architecture. The IA-64 architecture doesn't support this, so WoW actually converts your code to 64bit, but with a significant performance penalty.
*.NET code compiled to MSIL is JITted to the correct architecture. Probably the same happens with other architectures with an Intermediate Language like Java, but i'm no expert there.