The two most common reasons to update manually are if you process batches of changes to the data, or you have large spikes in the search load. If you process batches of updates you most likely want to update the index as soon as the batch is finished. Automatic updates have the potential to start in the middle of the batch, or wait for some period once the batch has finished.

If you have large search spikes, for example financial news sites may get their peak load in the morning before the market opens. Knowing that you would probably want to update the index right before peak load, and depending on the inflow of information, hold off updating the index till things quieted down.