There is no inherent reason to avoid such topics in fantasy. Throughout the history of fantastic literature (I am using the broader definition of fantasy, rather than that so prevalent these days of the "epic", quasi-feudal/mediaeval/pre-Industrial Revolution-etc.) writers have addressed various concerns, political, philosophical, metaphysical, religious, or sociological, and I see no reason why it can't be done in something such as you describe.
I would caution, however, that such concerns not override the storytelling and the quality of writing; else you end up with a sermon or diatribe rather than a story or novel and, while such things can sometimes be very interesting (e.g., passages in Pratt's The Well of the Unicorn and The Blue Star; Balzac's Seraphita; Lindsay's A Voyage to Arcturus; Eddison's Zimiamvian books; and so on), the audience for such is likely to be much more limited these days. Essentially, such must come from within the work itself, not be imposed on it. If it emerges naturally from the conceptions of that world and the characters, then it should work just fine. If not... it's one dickens of a pitfall to stumble into....
