Max -
The design waterline of a ship essentially assumes the ship's weight doesn't change between design completion and construction completion - an unlikely event. It may change later if changes are made, say, to the hull (such as blistering on ENTERPRISE in order to compensate for more weight and to improve stability.). For HORNET, the boottopping top during the Doolittle Raid was unchanged from the picture above with the sailors on the jetty. The ship has more weight aboard for the pictures of the Raid and so sits deeper in the water. USN ships were generally overloaded after the beginning of the war due to added equipment and AA guns not envisioned when the design was finalized.
Trump's oval portholes are the result of the molding process because the molds for the two sides of the hull come together horizontally where as the portholes in the bow area are at an angle to the horizontal of about 45 degrees due to the flare of the hull. You are correct to drill them out round.
This link should answer many questions for you:
http://www.hnsa.org/wp-content/uploads/2014/08/cv5.pdfThese are blueprints for YORKTOWN, and while she and HORNET were not identical twins, they are mostly twins. If you go through the entire CASF / 'calling all HORNET CV-8 fans' thread you will see a lot of discussion of the similarities and differences. For example, in the case of portholes, HORNET as commissioned did not have the same number of hull portholes as YORKTOWN. You notice in the drawing showing the Starboard exterior view of YORKTOWN in the link above, YKTN shows two horizontal rows along the length of most of the hull. These two rows are broken into two groups which are at different heights (Ignore the row under the forward pair of 5"/38 on the sponson). In the case of the two rows just under the Hangar / Main deck, HORNET was only completed with the upper row. Also, HORNET did not have any portholes in this row after the leading edge of the aft 5"/38 sponson, while you can see that YORKTOWN's portholes went much further aft in both the two rows under the Main deck. (Most of HORNET's hull portholes were blanked off with circular metal plates welded to the hull in July 1942.) Likewise, HORNET completed with only the upper row of port holes just under the focs'l deck, forward.
There are plans out there for HORNET sold by Maryland Silver. They are very complete and a bit expensive depending on your goals. The good news is that you will have a pretty complete set of plans showing most of the details you will need. The bad news is that you will have a pretty complete set of plans showing most of the details you will need. And those plans will show the conflicts between the real ship and the Trump rendition. If you are likely to lose sleep if I were to tell you that the porthole locations on the starboard side are not the same to the port side, then I shall not tell you that.
You see the situation here. Only you can decide how deeply to get into this. Tread carefully.