It is true that in order to fly an IFR flight in controlled airspace, Brussels needs to get a flight plan. 3 hours is a little extreme, and most flight plans can be turned around inside an hour if you have take the trouble to pre-validate the route.
Slots are issued 2 hours before EOBT for flights in the system already on a first-come-first-served basis. While there's no doubt that many if not most FPLs can be turned round quite quickly, there's a tactical advantage in getting the FPL in by then if things are going to get busy.