Hello Ricardo,
I'm not someone from the Pioneer team but I'm anal enough on music quality that I can reply you without a single doubt that Rekordbox does't perform any operation on the file itself (excepted the tags if you want it to do it), therefore the original sound quality of the file won't be changed.
To simplify, what Rekordbox does is basically take the ressources offered by your computer to analyse a file in depth and consign all these pieces of information into a database that can be easily read by a CDJ. CDJs aren't nearly powerful enough to analyse tracks (and play them at the same time), therefore if you don't use Rekordbox, the CDJ will only display pieces of information it can find by itself (that is name of the file, current BPM and past waveform I think).