If not having a special reason, never buy tickets for mountain excursions before having somehow reliable information on weather and visibility (meaning often enough just hours for Jungfraujoch) or you take chances being stuck with a non-refundable ticket for a trip at a bad time (weatherwise)
There is a passenger number limit set by the railway company for a day - should not be really a problem in September (especially not later in September).
In case you want to be on the really safe side you can buy a reservation for a specific train - https:/… - a bargain compared to the price of tickets you can buy then just before departure in addition to the reservation - or abandon reservation.Edited: 05 July 2018, 13:24
i am going in a few days and will try and go first thing in the morning to have the least crowds. ive been advised to make the decision the day before to see how the weather is.