May they would be a wish used in a prayer or during a toast or during some celebration. Let them can be an order and that appears more natural to me given the Czech sentence in question.
In English "May they remain there." is a kind of wish you express in prayers or celebratory speeches (e.g., toasts). It is not the same as "Let them remain there!" that is an order.
The Czech question without further context sounds more like an order to me. Or an ordinary wish, not that formal one. Not because of the form, but because of the content. But it could also be the formal kind of wish, we maybe we will add your answer as well.