On the original manifolds, I think those holes were blind (ie: didn't go through into the water jacket). Aftermarket manifolds may be tapped through. Big issue as I see it is exposure of the fasteners to water and the resulting corrosion.
Recommend you change the fastening configuration for your exhaust flange to studs and nuts. I'd make stainless studs out of set screws or all-thread and bond them into the manifold with JB Weld. Then use nuts to hold the flange to the manifold.
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