"Either he was on something untestable in the past, in which case it would presumably be something still not tested for, or he just wasn't ever using."
Or, he was on something testable both in the past and now, and for some reason never returned a positive test.
Or, he was on something untestable in the past but testable now, and now he has stopped.
Not saying one way or another, just suggesting other possibilities.
Regarding the injury thing, that is an angle that I have considered, having vaguely remembered that he used to be injured in his late youth...so I went to his wikipedia page, and noticed that he has been "injured" for essentially all of his professional running career, except for 2007-2009: leg injury for Athens in 2004, injury for Helsinki in 2005, hamstring injury for Melbourne in 2006, achilles and back injuries in 2010, back injury in 2011.
This type of injury history is what I have come to expect from very tall athletes who try to perform in power sports with lots of impact--I have seen it before, more than once. So on one hand, you could say that Bolt was able to perform as he did in '08 and '09 just as a result of his health status not getting in the way of his training.
But on the other hand, it is fair to ask why, or how, his health status improved during those years, which were coincidentally Olympic and World Championship years. It is well-known that 'roids and other such PED's speed healing, and the conclusion that he was using during that period is both rational and understandable, if not very convincing in the absence of other evidence.
His injury history is just another piece in the puzzle, although I won't speculate on exactly what conclusion to draw from that history.