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Program Files (x86) is the 32-bit program folder for applications, you're running on a 64-bit OS.
I don't know what changed in Cata, but I know with Wrath if you installed it on say Windows 7 64bit, it would tell you that the folder will be moved to C:/Users/Public/Games.
It doesn't hurt either way where you put it. The consensus behind the theory was availability of the application to all users of a computer by placing it in a public directory. Just another quarky Windows idea that really does nothing for you.
So the short answer -- you're fine, get on and whack some Horde.. or Alliance if you're the opposite.
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