The beauty of the poem is precisely that the speaker is not clear as to what the song means. The speaker is entranced with the song. Part of the reason that the song captures his imagination is because he does not know the words or the lyrics being sung. The inability to understand the lyrics allows the speaker to reflect on what the lyrics might mean. This is critical to the artistic message of the poem. Language is seen as a limiting function. To understand language means that an end towards moral and spiritual imagination is evident. If the speaker understands the song's lyrics, then his moral and artistic imagination is limited.
Yet, it is in not understanding the lyrics that the speaker is able to imagine what the lyrics might mean. It is in this light where most of the poem's imagery emerges. Not knowing the lyrics allows the imagination of the speaker to move to "Arabian sands" or to the "Hebrides" or to "the silence of the seas." All of these imaginative elements disappear if the speaker is aware of the lyrics. To this end, it becomes clear that if the speaker does not understand the song's lyrics and the song being sung. Yet, it is in this lack of understanding, a form of negative capability, that the greatest leaps in imagination can be taken.
No,the poet doesn't know that what the reaper is singing is singing about but he imagines that it must be something sorrowful.