There are no missable sub-quests and for the most part they will show up when you're navigating through your map selection. The envelope icon indicates that there is a quest available at that location so that part is straight forward.
Some quests have pre-requisites and will show up as available after completing other quests.
Spirit Temple ->
Another Hillside Anomaly ->
Otherworldly Visitors is one such quest-chain.
There are two that are somewhat
hidden and if you don't encounter them on your own they will not be displayed on the map. These two sub-quests are:
Beyond The Grave and
Into the Grotto.
Beyond The GraveAcquired by going to the
Tuah Seashore after you progress far enough with the main story and have reached
This quest will automatically pop-up when you enter the
Tuah Seashore map if the above condition is met.
Into the GrottoThis quest involves opening a door in the
Trench of Flames East Side area. In order for it to pop-up you will have to progress far enough into the story to battle the boss located in
Once you have defeated him he will drop a key. This will not start the quest but it will allow you to start it next time you enter the
Trench of Flames -> East Side area.