A simple example will do:
imagine you set up a First World War literature project - something relatively common in English classes - and you hand out (or ask learners to find) a poem by Sassoon, Owen or any of the famous English War Poets.
The poem will be 'about the First World War', or perhaps even 'about war' in general - but that is its surface level only, its topic. And beyond saying 'war is bad', there's little you can do with that topic (except fill in historical information, figures, dates and the like).
The theme(s) of the poem is something else: it is about the ideas a reader will have on the basis of the poem. The theme is about the treatment of the topic, and what can be said or thought about that topic.
For example, with WW1 (and, in fact, with most wars if not all of them), typical themes and their sub-themes would be:
loss (e.g. of life; of a generation; of youth; of spirit; of culture)
Patriotism (e.g. what is it, why is it there, what does it lead some people to do, individual life vs sacrifice for a nation)
Pain (e.g. of losing loved ones, of wounds, fear, psychological damage, after-effects, damaged-for-life)
Morality (e.g. of fighting; of killing during a war vs in a street fight; of killing to gain a few meters of ground; of fighting people like you; of sacrificing the youth to save others)
Society (e.g. gender roles; cultural and social changes; class (foot soldier vs officer); feminism and women's roles)
Those particular themes are not to be found in every poem of course, nor are they relevant to every text about the war. But this is about making a distinction between surface level (topic) and depth (themes):
thinking in themes helps you get more out of the text and - more importantly - out of your learners.
thinking in themes helps you create a running thread throughout your literature lessons; something you can go back to with another text to point out how a theme can be dealt with very differently across different texts, authors, periods or movements
thinking in themes helps you and your learners to consider one idea (one problem, one concept, one question) from multiple perspectives