"since there is only one log file per channel (if you ignore mIRC's log merging algorithm), each folder will contain one file"
Well not necessarily. mIRC has an option to date logfiles (by day, week or month) as well, so you might have many #*.date.log files in the folder, if there was a "Make channel folders" option they could be grouped...
Code:
/Logs
  |-	/Network
	    |-	/#channel1
		    |-	#channel1.20071001.log
			#channel1.20071002.log
			#channel1.20071003.log
			...
	    |-	/#channel2
		    |-	#channel2.20071001.log
			#channel2.20071002.log
			#channel2.20071003.log
			...

I wouldn't use it myself, but nonetheless, it isn't a bad idea really.