I think the film wanted us to guess if she fell and drowned or was she getting away from Sondro. With the prostitute near the end and we seeing what type of man he really was, she must have known he was rotten. This is now what her friend will have to contend with. Remember she said she did not care about her being dead, the film showed right after that she sees what she will get with Sondro. The loss of a friend and a cheater with Sondo
I think Antonioni made it quite clear in the film that Anna's disappearance made no sense at all. It's an island, therefore surrounded by water. The divers would've found her. What's interesting is not why she disappeared on the intradiegetic level, but why she disappeared from the film's structure.
People reacted with shock and surprise. The movie was booed at its Cannes premiere back in 1960, and amongst the many reasons why was Anna's sudden disappearance. Some other people got it, though: it ended up getting the jury prize.