I don't know about the Middle Passage, but I have some knowledge on how the VOC (Vereenigde Oostindische Compagnie = the Dutch East India Company) treated their slaves on longer journeys. The well examined case of the mutiny on the Meermin can give some insight. In short, the Meermin was a slave ship sailing for the VOC, in 1766 it set sails from Madagasgar with newly purchased slaves. Johann Krause (the supercargo aboard) was in charge of the vessel, in the VOC the merchant was the highest authority on board not the captain. When diseases started to spread among the slaves, which risked not only the potential profit, but also the health of the crew, Krause gave the order to unshackle the slaves and let them walk on deck. That order was not that uncommon, as the VOC rules allowed slaves to be on deck from time to time (The Durch merchants were mostly concerned with condition of their "commodity", the VOC didn't emphasize human rights or anything like that, that would be a modern and false reading of those rules). But most of the time the slaves where below deck, shackled. I hope my answer can help you with your question, even if it isn't about the Middle Passage. Source: Andre Alexander, “Shipboard Slave Uprisings on the Malagasy Coast: The Meermin (1766) and De Zon (1775)"