Color reproductions of the drawings in the Matthew Baker manuscript appear in quite a few places. Two others come to mind immediately. Bjorn Landstrom did his own color copies of several of them in his comprehensive masterpiece The Ship back in the fifties, and The Armada, a volume in the Time-Life Books series The Seafarers, contains at least one color photo.
The relevant volume in the Conway's History of the Ship series, Cogs, Caravels, and Galleons: The Sailing Ship 1000-1650, contains an interesting chapter called "Treatises on Shipbuilding Before 1650" by John E. Dotson. He has the following to say (p. 167) about the Matthew Baker manuscript: "At the other extreme [from the Portuguese works he discusses earlier in the paragraph] is the manuscript of Matthew Baker, now usually known as Fragments of ancient English shipwrightry. This manuscript was continued into the early seventeenth century by another hand. Baker was a master shipbuilder for the English royal navy during the reign of Queen Elizabeth I, and therefore well-placed and extemely knowledgeable about the design techniques of his day. He appears to have been influential in English shipbuilding circles. His notebook consists largely of the drawings which have been frequently reproduced, but contains little analysis of the way in which the moulds of hulls were developed. While the draughts are spectacular and informative in the ways that draughts and plans can be, the lack of text limits Baker's usefulness."
That probably explains, to some extent, why there apparently is no twentieth-century published edition of the Baker ms. But if some company were to publish a good-sized reproduction of the illustrations, with high-quality reproduction and scholarly commentary by somebody who knew what he or she was doing, I'd scrape up the money to buy a copy.
Another basic source on this sort of thing is Old Ship Figure-Heads and Sterns, by L.G. Carr Laughton. It was originally published, I believe, in the 1920s; it's one of the earlier examples of really serious, reliable research into the history of ship technology. Despite the title, the book contains lots of information about color schemes and decorative carving other than at the ends of the ship. (It contains, for instance, some interesting drawings of entry port ornamentation.) For many years the book was out of print, and the ship modeler who could find - and afford - a copy was an extremely lucky one. Fortunately, though, a nice, cheap paperback reprint has recently become available from Dover Books. Highly recommended.
Later edit: I just spent a few minutes trying to find the Dover edition of Carr Laughton on the web. No luck. Maybe that means it was unusually popular and the publisher sold out. I don't think I imagined it - but stranger things have happened.
I did, however, find another edition at, of all places, Lee Valley Tools. Here's the link: http://www.leevalley.com/wood/page.aspx?c=2&p=55449&cat=1,46096,46117
The price, for a hardbound book with color illustrations, is outstanding.
I'm not sure how the folks at Lee Valley got interested in publishing nautical books, but the company offers quite a few of them - all in high-quality editions at extremely reasonable prices. (The Lee Valley edition of Lever's Young Officer's Sheet Anchor gets my vote as the best I've seen.) For that matter, the entire Lee Valley site is worth careful study by any ship modeler. Take a look at the variety of woodworking tools - including dozens that are extremely useful for ship modeling.
Still later edit: I wasn't imagining things. Here's the link to the Dover Books edition of Carr Laughton: http://store.doverpublications.com/0486415333.html
Note that the price of the Dover paperback is actually a little higher than that of the Lee Valley hardback - but both are extremely reasonable.
The Dover Books maritime category is another wishbook for ship modelers. Love those prices.