My experience is with the Canon iPF6400, so it may, or may not apply, but I think chances are that its similar.
I noticed that if I don't print for 2-3 days, whenever it does start up, it wants to do a clean cycle. Using the excellent Prograf Status Monitor, I'm able to see exactly how much ink is used if I monitor it closesly. (ie. make a note of how much ink was used in total the last time I used the printer, and then look at the new total after it runs the clean cycle). I found that its about 14ml. This is the only type of clean cycle I have ever done. I know that from the menu, there is the option for clean A or B, so I assume clean A is this first cycle.
Now if I have not printed within 3 days, I don't want it to waste all that ink, so what I do is wake it up from sleep mode and shut it down. Then I start up in Service Mode, and do a nozzle check from the Service Menu that shows all the nozzles. It shows me of course if there are any clogs, but what I'm mot interested in is having the printing think its been printing. Then when I turn it off and start back in regular mode, it won't have to do a clean cycle because it would have known it just made a print.
I have also tried to do just regular nozzle checks every 2 days (without going into service mode), and this has the same action of doing a print, but after maybe about 2, it still realizes that it hasn't exactly done a print so it wants to clean. So the rule is try to do a print every couple of days, or at least a nozzle check, but sometimes you just gotta go into the service mode to get the clock to really reset into thinking a print has been done.
I have come back after the printer is off for a week, started up in service mode, did my nozzle 1 check from the service menu, noticed maybe a clog here or there, but did nothing about it. Simply turned it off to exit the service menu, and then turned back on into the regular mode so I could print. It didn't do a forced clean since I figure the counter/timer was tagged as just having done a print.
Now certainly if you see lots of nozzles clogged, then running a clean cycle isn't a bad idea. But after the printer has been sitting for just a few days, in most cases the nozzles are fine, and wasting 14ml of ink is quite a bit, and could be easily $7 or $8 minimum depending on the size of ink carts you use. That same 14ml of ink goes a long way to making prints. Its actually more cost effective to just print something every few days, especially on cheap paper, rather then running into trouble and having to do that clean cycle.
I also just replaced the printheads a week ago, and got exactly 2 years out of them, so what I'm doing can't be that bad.