The holes in the floors are limber holes to allow for drainage. They are drilled there because it is easier and they are guaranteed not to damage the hull there. (Yes, they are correctly called "floors" on a boat, not "bulkheads". Bulkheads divide the internal usable space into compartments,.. think 'walls' in a house. "Floors" are structural members that run athwartship and tie the keel to the stringers. Ok, my rant is over, now you can call them bulkheads like everyone else here.

. )
The holes in the stringers?,..... my guess would be for temporary lifting brackets at the builder ( lifting the hull out of the mold ?)