Some of the answers generally given are: The first and most common explanation is that in feudal days the people developed a custom of giving the suffix maru to the names of things of which they were particularly fond. Boys were called Takemaru, Kiyomaru, and so on by their parents. The Japanese also gave names to their swords, horses, musical instruments and other things, and these names also ended in maru, indicating that their owners had great love for them. Thus, it is explained, they followed this custom when naming ships.
The second explanation is that ships were regarded as floating castles, and thus were named as castles were. The innermost structure of a castle was called honmaru or main circle, the second and larger defense structure surrounding the honmaru was named ninomaru or second circle, and the outside defense line was called sannomaru or third circle. Regarding ships as castles on the water, they affixed maru to their names. And, the Japanese national flag, a red ball on a white ground, representing the sun, bears the name Hino Maru, lit., the round of the sun.
According to legend, some 5000 years ago during the reign of the Chinese Emperor Ko, the earth was visited by a heavenly being named "Hakudo Maru" who taught people to build ships. In gratitude and to insure celestial protection, his name has been attached to all ships since that time.
Again, Maru has been traced to the feudal years in Japan when surnames were denied to the merchant class, and it became necessary to add some distinguishing word to their shop names. The choice of Ya, meaning "the shop of," was used as a suffix and still continues to this day, i.e. "Sunya," or Mr. Sun's shop. A further distinction was needed for the name of the merchant's ship and Maru was adopted, thus Mr. Sun's vessel became "SUN MARU".
The first recorded vessels using Maru date from the Kamakura era -- 1192. Another creditable explanation appears to be the adoption of Maru as used in divination where it is expressed as a circle to convey the concept of perfection, i.e. heaven-earth, or completeness-in-itself. And what better designation of a ship than a little world complete unto itself?
It can easily be seen how these explanations, though different, have a common sentiment and could have developed from one and the same origin, but nothing certain is known.
There is one amusing point in this use of Maru about which you should be aware -- Japanese being written in ideographic form -- the vessel name is frequently written, as in the western usage, from left to right on one side of the ship, and from right to left on the other side. This balances the design of the writing so that the suffix Maru will be toward the stern from which ever side the vessel is viewed. But never fear, you are perfectly right, Maru is always the last word of the name.