For one, the exhaust has pulses, so the chips can be sucked in, as well as blown out. They can even be sucked up into the cylinder, then spit back out. When you drill a hole into the side of a pipe carrying a fluid at high speed, it may also cause a suction at the hole due to a venturi effect. It varies with where you drill it. I still think the safest is to have the motor off, then use a magnet inside the hole, until there are no more chips coming out.
The venturi effect is where there is an increase in velocity there will be a decrease in pressure. But when you have a pressurized manifold (which this is) the pressure is greater on the inside thus any hole will cause the pressure to move from high to low. The gasses in the manifold are contained and thus the venturi effect does not apply. Now as the gasses escape the manifold the pressure around the escaping gasses will create a low pressure area outside the manifold. As for the pulese, if you have negative pressure created by an exhaust port there is something very wrong with the engine. The pulses are actually pulsing pressure differentials due to the compressed gasses escaping into the manifold from the cylinders when the exhaust valves open, no negative or way to be sucked back in.