the Program files (x86) is where 32-bit applications are stored. 64-bit windows has a lot of funky redirects to make sure stuff still works.
For example- "C:\windows\system32"- when that folder is accessed by a 32-bit program, windows silently accesses C:\windows\SysWow64 instead. the "real" C:\windows\system32 actually contains 64 bit dlls and executables. (I know, it's weird).
same with C:\program files, except the redirection isn't quite so blatant: x64 programs get "C:\program files" as the environment variable, x86 programs get "C:\program files (x86)".