The lack of EGR could elevate the cylinder temps and in an extreme cases could raise the temps enough to warp the head, blow a hole in a piston. The cylinder head is alloy, the exhaust manifold is usually iron - cast iron at that. It's already inherently weaker than a forged unit but melts at a higher temp than aluminium alloy.
What could cause the intake manifold to crack? Overboost could, although it'd have to be way over the top. It doesn't get too hot that side of the motor so a dunking isn't likely. Other than that you're looking at physical causes like vibration or impact.
The exhaust manifold is different. A dunking in water could easily crack the manifold if it were hot - the turbocharger could also be affected. The pressure inside the exhaust manifold is quite high but I wouldn't have thought it would worry cast iron.
As for the connection: the EGR tube runs off a small port near the turbocharger inlet and comes around to the front of the motor where it is cooled by the engine's coolant (that's what the rubber hoses are for). It then connects to the EGR valve - not directly to the intake manifold.
I'd like to know where the crack is too, but I'd also like to know if the vehicle was used in river crossings, or full-throttle exercises for any period of time - anything that could raise engine temps. Please check the coolant level too - that could cause some trouble if it's too low.