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.
"Ať tam zůstanou" does not have the same connotation/use as "May them stay there".
"Ať tam zůstanou" is more like "I want them to stay there" or "They ought to stay there" - you can call it a wish, but it's more a demand.
"Kéž tam zůstanou" or more commonly with the conditional: "Kéž by tam zůstali" is more like "I wish they would stay there" or "May they stay there".