Because my hard disc was full, I've tried launching the game on 64bit without ksp_data files, and it didn't broke. It worked fairy well, the loading and construction and physics and all.
Seems like these two files, ksp_x64 data and ksp_data are identical except they use 32/64 bit os. Would it be a problem if I remove ksp_data?
(The files are in the Kerbal Space Program folder, in the 'common' in steamapps.)