Let's revise this - since I'm not sure if comparing the value of a ship and a map necessarily will accomplish anything (and isn't the important piece of information here). Not all ships are the same value (they vary in size and quality) and maps vary in quality and quantity of information provided. But, I think the core issue/question here can be summed up as: Were there highly valuable charts in the Golden Age of Piracy and why were they so valuable?

I suspect that at some point - since "Golden Age of Piracy" got mixed in here - that someone trickled down the story of Bartholomew Sharp and the South Seas Waggoner (but without the names or context). A Waggoner, or a Portolan, contains charts and directions to multiple places - and includes the locations of islands, cities, and so on. They often include particularly important pieces of information on getting there (like Latitude), where there are good harbors to anchor at in that destination, and potential hazards to avoid. This blog from the Royal Museums at Greenwich explains more about these kinds of maps.

Here is an example image of one of these charts - this is Isle of Juan Fernández. Well off the coast of the modern nation of Chile (over 400 miles), it was an excellent point to stop at for passing ships to acquire more water and even some food (especially after the Spanish put goats on the island for that purpose, so they would propagate naturally and be hunted down for food) without having to stop on the mainland of South America or near any settlements. Over the years in the late seventeenth and early eighteenth century, on two occasions, men found themselves stuck on this island alone. One was a man named Alexander Selkirk - the real life story that inspired the famous early eighteenth-century writer Daniel Defoe to write one of the most famous books in English literature Robinson Crusoe.

To explain how Bartholomew Sharp is involved, I'll utilize the prologue of the 1992 reprint of Sharp's Waggoner to explain it:

In 1680 a band of English buccaneers marched across the Isthmus of Darien from the Atlantic, or North Sea, to the Pacific, or South Sea. They captured Spanish ships in front of the city of Panama, one of which they made their flagship. From this vessel they terrorized Spanish possessions on the west coast of the Americas for eighteen months (mostly under the leadership of Capt. Bartholomew Sharp) and finally sailed around Cape Horn to the West Indies—the first Englishmen to do so from that direction. When they reached England early in 1682, Sharp presented to King Charles II a "great Book full of Sea-Charts and Maps, containing a very accurate and exact description of all the Ports, Soundings, Creeks, Rivers, Capes, and Coasts belonging to the South Sea, and all the Navigations usually performed by the Spaniards in that Ocean" (JP2 , 3:80).
That "great Book" was a prize of great military value indeed, because it contained just the sort of information that, since the days of Columbus, Spain had tried to keep secret from other nations—and it was almost certainly the source of Ringrose's South Sea Waggoner reproduced here. So when Sharp and two of his crew were arrested in London—accused by the Spanish ambassador of piracy and murder—there is some evidence that royal influence behind the scenes may have effected the verdict of not guilty, a verdict that eventually caused a minor diplomatic incident with Spain.

So there it is - this set of charts and instructions, taken by buccaneers and given to the English crown proved highly valuable since it revealed what the Spanish possessions were along the western coast of South America, Central America, and parts of North America. It also allowed, if so desired, for English vessels to bring trade or war to the Spanish more easily to that part of the world, whichever was desired.

Hope that answers your question somewhat.

Were there people who deliberately make low-quality maps to mess with folks?

To go on a side point that is somewhat related, the history of navigation in the 17th and 18th centuries is the history of trying to find an accurate means to determining longitude. It was only when James Cook went on his voyages with a chronometer in the 1760s and 1770s that accurate charts could be created. Cook created accurate charts of New Zealand and the West coast of America over the course of his voyages.

Before Cook and the chronometers, ships relied on dead reckoning or lunar distance to determine longitude. As these techniques were less precise, the charts they produced were less accurate and voyages in this era tended to try and stay within sight of land so as to be sure of being able to locate their landfall.