A captured spy usually didn't have to face a long prison term. In fact the concept of imprisonment for a crime was foreign during the Golden Age of Piracy. Typically prisoners were in the gaol (jail) while awaiting trial and then if found guilty, while waiting for the sentence to be carried out.
A gaol during the 18th century was not a very pretty sight. It was dark, it was dank, and it was overrun with rodents and insects. Most were just converted store rooms or cellars that were used as a gaol when the town had a prisoner.
Neither the temporary pen nor the permanent prison were a match for where England stored most of its criminals. The filthiest, most deadly prison of all was the prison ship. The prison ship was a derelict ship that was moored in a river or off shore. The ship was in such a state of disrepair that it was not worth salvaging. Prisoners were thrown into the hold and left to rot until they were tried and their sentence carried out.
Sanitary conditions on the prison ships were abysmal. The ships leaked water, making the men was constantly wet. Vermin such as lice, spiders, other insects and larger critters such as rats were all over the place. Disease was constant with many prison ships cesspools of cholera, tuberculosis, and typhoid fever. It was not uncommon for a healthy person to enter a prison, be acquitted of his crime and then suffer from a chronic illness for the rest of his/her life; because of his short time in incarcerated.
The jailers were not too concerned about removing the dead and other prisoners were not quick to report a dead person for fear of even less food being thrown down the hold. Few people could make it past a month on a prison ship..
In all types of prisons, some of the more dangerous or more important prisoners were kept in chains at all times. Some would also be chained to the wall or other large object. If these prisoners happened to have enemies in the cell with them they would probably wake up dead the next day. This was most unfortunate but it was something the authorities could live with. The only bright side is that once you were tried and sentenced, your days in the gaol were numbered. It was time to be flogged, pilloried, sold or hanged!
You can ignore the numbers and letters on the log book as it was used for the event only.