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I don't know all the specifics of Y-block bolt holes, but it is common for bolt holes to go into the water jackets of engine blocks. Chances are, what you experienced is perfectly normal. When you put it back together, be sure to use a sealer on the bolt threads, to prevent leakage and seizing.
I had a set of rebuilt heads that the rebuilder must have cleaned the valve cover bolt holes out with a power driven thread tap, right into the water jacket! The hole had a bit of a bottom on it so with an Allan head set screw and some JB weld I put a plug in the bottom.
If yours doesn’t seal with the bolt you might think about epoxy-ing a plug at the bottom of the hole if there is room?