A. I think we're probably reading more into it than there is. We are humans, and we've evolved to see more patterns than exist in reality (better to see a non-existent bear and live than not to see one that is there).
B. The logic for ACARS messages is published, we're just trying to use them for something they were never intended to do. They're there to report aircraft position, status and issues that may require maintenance. They're not there to record flight data.
C. There's no secret, but I wonder how much experience there is with A330s reporting exactly this set of ACARS messages. Again, we're only getting a few indications here.
You can't really rule stuff out here. For example, we can't say "they didn't fly into a huge cell, because if they did, they would have seated the FAs and everything would have been secured." We can't say that, because our weather data suggests exactly that, and if they had seen what our weather data shows, they would have gone more than a little bit off-track to avoid it, as the other aircraft did.
If the evidence shows that they weren't belted in, all that tells us is that the flight crew were not expecting turbulence, which is a state consistent with flying through a huge cell (that is, not being aware of it; another state consistent with flying through a huge cell would be being aware of it, but underestimating its intensity).
In any case, what about the other flights that were threading the thunderheads in the ITCZ that evening? Did they secure the cabin?
We can't argue that 39 flights in an A332 implies familiarity with the wx radar if there's formal training or evaluation on using it.