Although it seems "natural" for a rabbit to drink from a bowl, water in a bowl is out in the open and subject to foreign bodies including the rabbit's own emissions.
Water in a bottle usually stays fresh longer, (i say usually because sometimes food (especially crunched pellets) in the rabbit's mouth can end up on the ball, then get pushed into the bottle that way) and it can signify them drinking from a stream, their water source is not always underneath them, such as a puddle, stream or such, in the wild.
Bottles, if cleaned every day with fresh water added afterwards, are far more hygienic than bowls.