It's likely that many authors consider themes when writing their manuscripts, also. There are "issue" books in YA and middle grade--books that focus on divorce, drugs, peer pressure, etc., just like the infamous after-school special. But even outside of "issue" books, themes crop up when discussing and pitching all kinds of fiction: YA and adult; commercial and literary. I see the touchstones of these themes in query letters--words like "loss," "self-discovery," "grief," "journey into manhood," etc.
Now, if you were worried that I was going to add ONE MORE THING to your query checklist, have no fear. I don't think theme needs to be mentioned in a query at all. You can scratch it off your list. That being said, if you feel it's important to mention theme in your query, give your query letter a few extra double-checks before you send it out.
- Does your mention of theme add a unique element that you can't add through plot or character description/summary/pitch?
- Or does it rely on clichéd, broad tropes to do your dirty work instead of the fresh, specific language of your story, your plot and your characters?
The best themes are subtle and incite conversation, maybe in class, over a post-dinner port, in book club, or with your critique partners/agent/editor while revising your manuscript. So be a little judicious in employing theme in the query letter. Otherwise, an agent might think that your manuscript has a didactic tone, not an engaging plot, and you might not get a chance to have the discussion about theme during revisions.