The best theory, in my mind, as to what happened on the Mary Celeste can be found at:
http://www.deafwhale.com/maryceleste/
In short, the ship was hit by a seaquake, a maritime version of an earthquake. This shook up the crew (both figuratively and literally) and the ship. Inspecting for damaged they noticed the 9 leaking barrels of alcohol and smelled its fumes. Fearing they were on a potential bomb, they threw open the hatchs. As a further precaution, the entire crew got on board the lifeboat to wait until some time when it was deemed safe to reboard the Mary Celeste. The lifeboat may or may not have been tied up to the ship. But somehow, due to bad weather or another seaquake, the lifeboat became separated from the Mary Celeste.
However abduction by the hollow-earth Nazis is a good theory too.