Found this on their websites:
"A smaller bottle is more hygienic. A larger bottle that is not finished might be kept open, thus a bigger risk of infection with other bacteria..." - Yakult Malaysia
"Opening and closing a larger bottle on numerous occasions can result in a decrease in the number of live probiotic bacteria due to the introduction of various air-borne bacteria. This is undesirable because bacteria have the potential to compromise the quality of Yakult..." - Yakult Australia