Yes, they do. Part of the OpenType standard are the so called “OpenType features” which (amongst other things) allow for contextual alternates, i.e. different kinds of ligatures, and for stylistic alternates, e.g. a slashed zero, a single-storey ɑ, etc. All of these different glyphs are encoded in the font and can be enabled when typesetting using different selectors. This website shows them off.
Some ligatures, like “ffl”, are a separate character in Unicode. Some were added because they can be considered a different character in languages other than English. Some (like “ffl”) were added because of legacy reasons; “no more will be encoded in any circumstances”.