In English, "Where are these ducks flying?" can have two meanings.
The first meaning uses "where" for "TO which location" (destination of movement), so the sentence means the same thing as "To where are these ducks flying?" or "Where are these ducks flying to?". Since the sentences mean the same, it should not be surprising that they are the same in Hungarian. This "whither? where to? where?" meaning is hova in Hungarian.
The second meaning uses "where" for "AT which location" -- the answer might be "over the house" (perhaps they are flying round and round in circles over the house without a destination; the flying simply takes place over the house). This "where?" meaning is hol in Hungarian.