You're certainly right about the Academy "Roman Warship." It is, in fact, a reissue of an old kit by the late, lamented, excellent Japanese company Imai. It's beautifully detailed and engineered, but, as you noted, too short for reality - and the arrangement of the oars doesn't make sense. (It has the "sponson" arrangement of a bireme, but only one bank of oars.)
At this time there is no reasonably accurate ancient galley kit on the market. To be fair, a big part of the reason for that is that the scholarly community has done a lot of rethinking about such ships in the past few decades - largely due to the information gathered in the course of the building and operating of a full-scale replica trireme, the Olympias. (Oh, for a kit that was a genuine scale model of that ship!) Recommendation: enjoy, but take it with a grain of salt. For the current scholarly thinking about what ancient warships did look like, an excellent place to start is The Age of the Galley in the Conway's History of the Ship series.
Heller's "William the Conqueror" is utter nonsense. It's a slightly modified reissue of Heller's miserably misproportioned "Oseberg ship" kit. There's no way the ships of William the Conqueror were shaped like that. Unfortunately nobody knows much about what they did look like. The only contemporary representations are those in the Bayeux Tapestry, which don't help a lot. I talked this one over sometime back with our university's resident expert on medieval ships, Dr. Tim Runyan. He confirmed my impression that a French ship of 1066 almost undoubtedly would have been beamier, and had a great deal more freeboard, than the traditional concept of the "Viking longship" - which is what Heller apparently was trying (with little success) to reproduce with the kit on which its "William the Conqueror" was based. Recommendation: avoid.
Trumpeter Zheng Ho Treasure Ship - I know absolutely nothing about East Asian vessels and can't help with this one.
Zvezda cogs - You got it. I don't know much about the subject, but people who know more than I do have commented about the deck planks. They also acknowledge that, since the cog was such a common ship type in so many places for so long, it's entirely possible that not all of them were configured identically. Recommendation: build it and trust it, but change the deck plank configuration when you paint it.
Heller Nina, Pinta, and Santa Maria - nobody knows much about the real things, and the Heller versions are probably about as good as any of the other reconstructions. Recommendation: they're ok - but do note that two of them use the same hull.
Airfix Mayflower - a nice, believeable kit. Recommendation: trust either it, the Revell version, or both.
Revell "Man-of-War" - Revell has sold two kits under that label. The big one, labeled "Elizabethan Man-of-War" (about two feet long) is junk; it doesn't meet any reasonable definition of the term "scale model." The smaller one, labeled "English Man-of-War" (about 18" long) is a modified reissue of the Revell Mayflower. It's a bit hard to swallow as a genuine warship, but I suppose it's possible that a ship like that could have existed. Recommendation: avoid the big one at all costs. Regard the little one as an alternative, eminently believable model of a small, late-sixteenth- or early-seventeenth-century merchant ship with lots of guns.
Heller Golden Hind - It's a reissue of the Revell kit, which I personally regard as one of the best plastic sailing ship kits ever. The most recent research suggests that it may not have quite enough guns, but otherwise it is, in my opinion, an excellent interpretation of a ship about which almost nothing is known for certain. Recommendation: build and enjoy, but if you want to make a painting of Drake's fleet you need to do some reading. (Harry Kelsey's Sir Francis Drake: The King's Pirate is the best place to start.
Heller "Spanish Galleon" - Heller put that tag on several of its kits, most of which have interchangeable hulls and various other parts with different decorations on them. I don't have much faith in any of those kits, but with some careful work they might be made into believable models. Again, so little is known for sure about this ship type that it's tough to pronounce any model "right" or "wrong." There's general consensus, I think, that the best "Spanish galleon" kit on the market is the one from the late-lamented Imai. Unfortunately it's hard to find.
Lindberg "Sir Henry Morgan" - like most other Lindberg sailing ships, this one is a marketing ploy. It is in fact a reissue of the old Pyro seventeenth-century French warship St. Louis. As such it generally resembles the real ship, but it's a pretty basic kit. Recommendation: if you're looking for a representation of a large French seventeenth-century warship, it will probably do. But Airfix and Heller both make better St. Louis kits.
In researching stuff like this, an excellent place to start is the 12-volume Conway's History of the Ship series. It contains up-to-date articles by eminent scholars, lots of illustrations, and useful glossaries. In its original, hardback form the entire series was quite expensive, but it's been reprinted in paperback. Used copies of the individual volumes can also be found, for somewhat more affordable prices, on the web. There are, of course, dozens (if not hundreds) of other books that take up the individual ship types, but the Conway series would be an excellent starter.
Hope that helps a little. Good luck.