If items are light and soft I don’t see much harm but I’d prefer to use the cockpit rather than the end hatches and to secure (tie in with cord) any light but hard items, like paddles. Many people seem to overload clamp-on racks and SUV manufacturers’ flimsy racks – check your rack’s rating and think about what will happen if you are in a serious collision. Flying roof loads have been known to cause fatalities and serious injuries when the collision itself would have otherwise resulted in no injuries at all.
As Mick says, do something to keep out rain from the cockpit – (not to keep your seat dry – as was once suggested to me!) – but to prevent several kgs of water from accumulating and sloshing about, possibly causing a dangerous stability or overload problem. This is one reason for preferring J bars or carrying the boat inverted (like all canoeists!)
There are serious safety issues with roof loads on closely-spaced passenger vehicle racks. Strong end ties are essential, mounted to a solid part of the vehicle, not to the rack, (which have been known to break or come loose) but on some vehicles it is hard to find anything that I’d trust as solid!