The dual structure is by design. Having 32-bit programs installed to the "Program files (x86)" folder eliminates the risk of having both 32-bit and 64-bit installs of the same program present, and their installation files creating conflicts and/or performance problems.
Some programs install both 32-bit and 64-bit versions, so I suggest you leave the structure as it is.
If, on your machine, both folders are almost duplicates (Have you compared sizes?), it mean that most of the apps you have installed install both platform versions.