Were there privately owned merchant ships, or were all/the majority of them owned by big trading companies?
In either case, were actual merchants brought on board and were these merchants the ones who dealt in trade once they docked in foreign shores? If there were "independently owned merchant ships", how likely would it be if the captain himself was the who conducted trade, buying goods from one port and selling them in another?
Or were merchant ships little more than cargo ferries that carried goods that had already been purchased (or been agreed to be purchased) from point A to point B? For instance, trading company X has an agreement to buy silk from trading company Y in India, and simply sends a ship to pick up the goods and pass along the fee.
There were lots of privately owned merchant ships, but the big trading companies, such as the East India Company, also owned their own ships. (The East India Company had a legislated monopoly on all trade between Britain and India from 1600 to 1818 (1838 for tea), and usually carried this trade in its own ships.)
The big trading companies were an exception to the general pattern that by the 1600s, ship owners owned ships and merchants did not own ships.
This may have been somewhat different in different parts of Europe, but in England, looking specifically at Bristol, we see that by the late fifteenth century, it would be increasingly unlikely that a merchant would buy a ship to help his business and sell his products internationally.
Early in the fifteenth century many merchants were ship owners (most often in the form of owning shares in one or several ships, though sometimes owning a whole ship). For example, in Bristol, Walter Derby left his servant Nicholas half shares in two different ships and split a half share in another between two other servants. Thomas Sampson left his cog "Joan" to his wife Joan.
Source: Eileen Power and M. M. Postan, "Studies in English Trade in the 15th Century,"
By later in the century, however, specialization had become more common. A wealthy class of ship owners emerged in Bristol. These men sometimes owned ten or more ships and did not buy or sell goods, but made money from charging for carrying the goods for others.
William Canynges, for example, owned 10 ships and kept 800 men employed in Bristol in the late 15th century.
Carriage was expensive, with examples of one pound and of 21 shillings per tun being charged for the transport of wine from Bordeaux to Bristol.
Risks were high, from being lost to storms, to enemy action, or from having your ships commandeered by your own monarch to transport some of his army.
There was no insurance. Diversification of risk probably meant that a wise merchant would not own a ship outright. He would either own shares in several early in the century, or would pay to have his cargoes transported later in the century by the ships of a specialist shipowner, who diversified his risk by owning many ships.
The ships owned by these large shipowners were generally called "navis" or "batella", but whether cog, caravel, nao, or carrack it is difficult to say.
They were probably fairly large ships, circa 300 tuns. The largest ship mentioned in these Bristol records was the "George" of 511 tuns, which carried a cargo on her maiden voyage worth more than 1000 pounds sterling. This cargo was made up of goods from 63 merchants. If the "George" was charging a pound a tun, carriage cost half as much as the value of the cargo.
This again illustrates that it was not common by the late 15th century for individual merchants to own their own ships. The age of specialization had set in. Merchanting and Shipowning are different businesses, and it had obviously become more profitable to specialize in one or the other, rather than trying to do both.
At various times, especially when exploring new markets (but also in some trades like (frequently) the slave trade), ships would venture speculatively, carrying a cargo to try to sell and hoping to pick up a return cargo to bring home and make a profit. For example, ships from Salem Massachusetts did this when exploring the East Indies markets soon after the Revolution (since, after Independence, they were free to try to break the East India Company monopoly). In this case, either the captain would make buy and sell deals for the cargo, or, more commonly, an individual known as the "supercargo" would be on the voyage, appointed by the merchants who had consigned goods to the ship, to negotiate buy and sell deals on their behalf (he was usually rewarded with a cut of the profits).
Once trade routes became more known and predictable, these speculative trading voyages became less common.
So, to summarize, here were the possible patterns:
A large trading company owns its own ships to carry its traded products.
A shipowner owns ships and charges merchants transport costs, or charters the whole ship to a merchant or merchant consortium for a voyage (the most common arrangement on established trade routes, at least for English ships).
A shipowner (usually in partnership with merchants) agrees to a speculative voyage where goods will be bought and sold and the profits (if any) divided according to a pre-agreed formula (fairly common, especially for exploring new trade routes, and for smaller ships).
A merchant owns his own ship (but makes his money through trading) this might be used in certain trades where specialist ships (fast ships, armed ships) were employed or the trade was to some extent clandestine (like the slave trade after it was outlawed by the British and Americans in 1807, or smuggling).
Fishing and whaling ships were owned by a shipowner (sometimes the captain), or ship owning consortium, and the profits of a voyage divided by formula between the owners and the crew.