"Drown" is one of a family of verbs (known as ergative, labile or middle-verbs) that has both transitive [with an object] and intransitive use. But the meaning is a little different:
This means that John is dead.
Mary drowned John
This also means that John is dead; he was murdered by Mary.
This means that the passive form of the second sentence
John was drowned (by Mary)
Means that John is dead.
So both "John drowned" and "John was drowned" mean that John is dead. The difference is that the second sentence implies that someone murdered John. The first sentence doesn't indicate how John drowned.
So, to compare your sentences the difference is that "They had been drowned" implies that someone had murdered "them". If you don't want to create this implication then: "... because it was assumed that they had drowned" is correct English.