Using boats for traveling -- Is there any advantage?

The main advantage of a boat is that it's a lot faster and safer than swimming.

There are basically 2 main reasons in terms of utility to use a boat:

Secrets in the water
You'll find some secrets that are far out in some lakes or the ocean that are either tedious to swim to or even dangerous since there are a lot of drowners on the way there. Boats allow you to "ignore" drowners whereas swimming and diving requires you to fight them with your crossbow

Quests
There are some quests (IIRC even a main story Quest) That require you to go to an Island. Again this could be done by swimming but you're much faster/safer if you use a boat to reach the destination. Once you've unlocked the fast travel to an island you don't need a boat anymore though.

Also: Sailing is fun. Who doesn't like to relax on a boat after a long day of butchering werewolves and drowners?

The relevant uses for boats are:

• boats have separate fast travel locations outside of the signpost network, indicated by anchors on the coast line. These can be fast-travelled to at any time while commandeering a boat
• to save time when traveling prolonged distances on open water (i.e. mostly Skellige)
• to allow for safer travel by outpacing some waterborne creatures (sirens are still a problem)

With the exceptions of very few quests (as mentioned e.g. A Towerful of Mice), boats only offer comfortable means of travel on open water. Not using them does not impede your progress in any way.

In Velen and Novigrad there is no real need to use boats and you don't miss anything. An exception to this is the 'A Towerful of Mice' quest where you will need to use a boat. There are a few markers out at sea but you can choose to swim or use a boat for these.

Once you get to Skellige there are lots of islands and markers out at sea and you will need to travel by boat (or swim).