during the last 30 seconds when inbounders can throw basketballs over the inbounders station and try to score, do the balls count if they bounce off the floor into the basket?
Yes.
It does not say how the Basketballs may come to pass through the Hoop; therefore their travels to the goals are irrelevant. Bounce away!
You can even bounce it off the other guy’s robot to get it in. It would still count.