From what I have read here on the forum, most of the exhaust manifold leak problems are due to corrosion from salt water and not properly flushing with fresh water after use and/or age. Like pwgsk said, they are supposed to be self draining but most of us still flush them with antifreeze for winter just to be on the safe side. If it was cracked and leaking it could let water pool in cylinders after it was shut off. While running I would think exhaust back pressure would keep any water from entering.
As for a leaky intercooler, that definitely could have burst due to improper winterization. They also go bad on their own sometimes. I noticed in your earlier post that you have some Riva mods, do you have OE intercooler or aftermarket? Either way, your issue may warrant a leak test just to rule things out...