Looks fine to me, and yes, I’m sure those little holes are there just to be sure any water that might get up there drains out easily. I guess I have never taken the time to look closely at this area, but will surely do so the next time I work on one of these engines…
That sure looks like a low hour fresh water unit to me, the big hole you were worried about was probably just a casting flaw, and nothing to be concerned about, it is nowhere near any cooling passages.
Please take a moment to ensure the shift lever bellcrank is tight on the shift lever while the powerhead is off. These aluminum bellcranks like to loosen up/crack creating slop in the shift handle…don