Of all men on the ship, who could have put the carved head in the hold?

Since the text does not reveal who put the carved head in the hold, we can only make guesses as to who may have done so. While Mr. Barlow could have placed the head there, it is also possible that another member of the crew did so. 
Whoever put the head in the hold clearly did not want Charlotte to explore the area. In chapter 6, Mr. Barlow warned Charlotte about going down to the hold. When she questioned him, he mentioned that the hold contained extra cargo. However, he also warned that there were rats, roaches, and "foul bilge" down there. Additionally, Mr. Barlow mentioned that the brig or the "ship's jail" was located in the hold.
He cautioned that Captain Jaggery never sailed without a brig on board. This new knowledge made Charlotte uncomfortable, but Mr. Barlow might have intended his words to elicit this reaction from her. It was while Mr. Barlow was helping Charlotte retrieve her trunk that he took the opportunity to warn her about Captain Jaggery. According to Mr. Barlow, the captain was not what he seemed. Mr. Barlow also divulged the fact that Captain Jaggery was abusing his crew.
Prior to Mr. Barlow's warning, Zachariah had also warned Charlotte about the captain's misconduct. However, Charlotte refused to believe either man. It is entirely possible that either Mr. Barlow or Zachariah could have put the head in the hold. The men might have wanted to spare Charlotte the sight of the filthy prison.