Under the Air Navigation (Foreign Military Aircraft) Order, 1952, the Minister for Foreign Affairs is responsible for regulating the activity of foreign military aircraft in Ireland.
The strict conditions applied to requests for permission for a foreign military aircraft to land routinely include stipulations that the aircraft must be unarmed; must carry no arms, ammunition or explosives; must not engage in intelligence gathering; and that the flights in question must not form part of a military exercise or operation.
As to whether troops who participated in a particular military exercise may have passed through Shannon on a civilian aircraft at a different time, either before or afterwards, that is not information which is available to me.