1. #3. I can think of a dozen problems with this configuration (most of them have to do with sail handling and with deck management in heavy weather). Therefore for me, #3 is out.
2. Number two is better. But, the main purpose and function of the grating is to let air into the lower decks. I am not quite sure what the purpose would be in eliminating one-third of the grating and installing a garden fence gate in its' place (especially since you end up with three constructs when the job could be done just as well with two - one fence gate and one grating). Also, there is a 'standard' for deck grates and covers that has planks'
running parallel to the keel or perpendicular to the keel (usually not both) depending upon how the frames, beams and carlings are structured. . There is also a lot of woodwork that supports the ends of the planks in gratings and like structures. There would probably be no supporting structures for the end of the solid boards (unless, of course, you wanted to spend a lot of time energy and money to build totally non-standard decks for no practical gain other than just for the 'hell-of-it'). Also consider that the owner paying the bill would fire you on the spot in a hot second if he observed that the ships chief constructor had absolutely no idea how to build a ship to an almost 'standard' design that had proven itself over a period of about 2,000 years.
3. Therefore, I vote for fir #3 (even though it has problems that would have eliminated it as acceptable at the time) . Number three still has the 'fence gate boards' running in the wrong direction, but it is the best of the three. There is also one other problem, The two supports for the boat would have been at the ends of the hatch coverings and they would have rested on the deck (which is built strong enough to support the boat) and not on the hatch coverings (which would not be strong enough to support the boat). The first heavy seas will probably send the boat directly into the bilge. If you made this change, you could also position the boat along the centerline of the ship, which actually would have been where it would have been positioned. With tthis configuration you can remove the hatch covering planks, access the below deck areas and conduct the ships work with the least amount of unnecessary disruption to the ship's routine. I really think you should make a #4.