I heard these banca boats can be dangerous during high waves. How safe are they?

You can check out our weather forecast page for an idea. Storms occasionally pass through the country between June and mid November, after which the dry season starts and the seas are generally very calm. 

In the event though that the weather gets a little rough, first of all your captain will never risk his boat, because that is his livelihood. The local coastguards are also vigilant and do not even let the boats, nor the bigger ferries, leave dock. This is rather rare. But other times the waves can get a bit choppy but are not dangerous at all. The banca boats have broad wings on their side and the captain knows which path of least resistance to take between the myriad of islands. Among the 52 islands along the way, there is always a shore nearby where to shelter.

If you are concerned about your fancy electronics getting wet, there is a waterproof storage area under the deck, and it is always advisable to store them in a quality wet bag. They are inexpensive abundantly available in the area.