Ortiz was subject to random testing for the last decade of his career and never failed a test.
The difference between official testing and the preliminary testing in 2003 is that now the athletes can request that the sample be retested. There are also well-defined rules for the collection and handling of the samples. A positive test from before those developments is not nearly as reliable - and thus not as damning - as a failed official test.
That doesn't mean Ortiz wasn't using in 2003, and it doesn't exonerate him if he was. But with no other evidence against him, it's not clear or irrefutable proof he was using. 10+ years worth of passed random testing suggest that he was very effective for a very long time without PEDs.