How much and how often you clean your pens are up to you, but I think it is a good idea to do it now and then.
I try to do it myself not every time I refill my pens but every other to every third time. And I only do a full “flush water in and out until its 100% clean” when I change inks. I just flush clean water through the pen a few times before I refill it. Takes less than a minute per pen.
If you are using a cartridge converter type pen, then there is no damage to cleaning it every time you have the opportunity. But the more often you clean a piston filler, the shorter time it is between each time you have to grease the piston.
Like with everything else, there is something that is too much and something that is too little; the trick is to find a place in the middle.
You probably know why, but I am going to explain it anyways. The reason you want to flush water through your fountain pen from time to time is to make sure nothing dries up in the feed of your pen; and that is bad because it blocks the ink from flowing through your pen and onto the page.
If you use a piston or a converter, just suck water in and out a few times, and use a bulb syringe if you use cartridges.
But the most important thing is to do a thorough cleaning when you are switching inks. The first reason should be obvious to everyone, but it is to make sure that you see the proper colour of your new ink and not some weird mix between the old and new. But even more important is to make sure that your pen are completely clean when you start using your new ink, because some inks don’t mix that well. Everything from combinations that actually can damage your pen to combinations that clog up your feed.