What are ligatures, and should I leave them on?
Set the word fine in a serif face and something awkward happens: the hook of the f runs into the dot of the i. They fight for the same piece of space, and you get either a collision or an ugly gap.
Type designers solved this a long time ago by drawing one joined shape for the pair — a ligature. The most common are fi, fl, ff, ffi, and ffl. Printed books have used them for about five centuries, which is why a page set without them can look subtly wrong to someone who has never heard the word.
Leave it on
It costs nothing, it's invisible when it's working, and it's what every professionally set book does. The formatter has it on by default, and the export report tells you how many distinct joined forms your book actually used.
What it does not change
Ligatures are a drawing decision, not a spelling one. Your text is unchanged: the PDF still contains the letters f and i, so searching for "fine" finds it and copying the text gives you back real words. Nothing about your manuscript is edited.
When you might turn it off
Rarely. The one real case is a typeface whose ligatures you dislike on inspection — look at a chapter of the free watermarked proof at full size and judge it there rather than on screen at 100%.