There was lots of discussion on this at the time of TWA800 investigation
Most agreed it was a very small chance to encounter one and of course there was no evidence of craters in the top of the fuselage.
Regarding the discussion about the speed of sound above.. I guess you would need to convert this discussion to one of actual velocity in order to make judgements. Then one needs to estmate the most likely particle size moving at this velocity.
It's easy to speculate on what if's but a lot more practical to speculate on at least the more likely scenarios that haven't happened yet (or have they)