Sim, o fail2ban continua monitorando arquivos de log rotacionados. De server/filter.py
439 ##
440 # FileContainer class.
441 #
442 # This class manages a file handler and takes care of log rotation detection.
443 # In order to detect log rotation, the hash (MD5) of the first line of the file
444 # is computed and compared to the previous hash of this line.