Hi -
This is an interesting detail that I've bumped into several times during the past twenty years or so. I don't pretend to have a definitive answer, but I think Heller may be right in omitting the entry ports.
The Victory, like most other preserved ships, has been modified many times since - and before - the Battle of Trafalgar. Heller tried to reproduce her appearance at that time (1805). Pinning down exactly what she looked like at that date is quite a project; the exercise has to be based on documentary and pictorial evidence, and on some guesswork.
J.M.W. Turner went on board the Victory shortly after the battle and made sketches for his enormous painting, "The Battle of Trafalgar," which is in the National Maritime Museum at Greenwich (and reproduced in most illustrated books about Nelson). It shows the ship's side exactly the way Heller does. So does the contemporary model in the same museum - a model that supposedly depicts the ship after her major refit of (I think) 1802.
The most recent book about the Victory is the one by Alec McGowan and John McCay. In addition to Mr. McCay's magnificent drawings (some of the finest I've ever seen), it includes quite a few reproductions of contemporary paintings of the ship. Not one of those paintings shows the entry ports. The text of the book doesn't mention the point.
I wouldn't want to stake money on it, but I am inclined to think the entry ports were installed sometime after the ship was taken out of active service. If I were building a model of her in her Trafalgar condition I'd leave them off.
Hope this helps.
Best,
J. A. Tilley
Dept. of History
East Carolina University
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.