You are correct that the log files have the same names (since they are based on the monotonically increasing backup ID on each site). If multiple backups with the same backup ID try to run at the same time your log files will not make sense – the lines will be mixed from two or more backups. Otherwise logs will simply be overwritten.
It's best to have one subdirectory per site inside your big backup repository.
Not just for the log file naming, but also for filesystem performance. After a few hundred files filesystem performance starts to degrade, with simple things like listing the contents of the folder taking several hundred milliseconds. This is easy to reach if you have, for example, a backup that consists of around ten parts and have a quota setting that allows forty or so backups to be present at the same time. Do this for thirty sites and you will be experiencing slow access to that directory. Using subdirectories reduces the number of files per directory, meaning you are unlikely to experience this issue.
Nicholas K. Dionysopoulos
Lead Developer and Director
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