FIRST
Dirk and Jake expect to see them in dreams
In the first sentence, them refers to some unnamed others (other people or things).
Dirk and Jake expect to have a dream about those people or those things.
SECOND
Who do Dirk and Jake expect to see them in dreams?
them in the second sentence could refer back to Dirk and Jake or to some unnamed others.
If them refers to Dirk and Jake, it could be paraphrased:
Who do Dirk and Jake expect to have a dream in which Dirk and Jake appear?
If them refers to some others, it could be paraphrased:
Who do Dirk and Jake expect to have a dream in which [those people or things] appear?
Those others could be "Mike and Ike", say, or two or more nouns (plane and train), or a single plural antecedent noun, supplied in the context: "chickens, zombies, boats, flowers, mountains..."