On our SQL Server theres a SQL Job which is ran every hour. On one particular hour it doesn't seem like the SQL Job was ran, and that was due to the SQL Server Agent being stopped during a backup.
If SQL Server Agent has been stopped, are the jobs which are supposed to be ran during the time its stopped simply ignored, or ran later when SQL Server Agent is running again?
They are ignored.
You can set up a schedule to start automatically when SQL Server Agent starts if you want to do some custom logic here such as checking for missing runs (and you can assign multiple schedules to a job)