Jeff, can't be certain, but possibly these holes are the location of spot welds between front and rear components of the bulkhead. They've been drilled out to enable dismantling and treating internal rust. In my own case the bulkhead was badly rusted under the "weaver seal" so much so that the gap opened and closed with the turning of the steering wheel. So I had a piece of sheet steel folded up to go the full width under the windscreen and down behind the trailing edge of the bonnet. Pop rivetted in place it really stiffened up the bulkhead. Back to your vehicle yes I'd use silicone sealant to keep water out of the double panel.
Cheers, RobS
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