Yes brake fluid absorbs moisture from the air so flushing would be a wise idea. Likewise I believe few people flush the brake system unless the brakes give trouble, me included.
Personally every master or wheel cylinder I've ever taken apart the majority of the damage to the bore has been in the bottom. I doubt flushing would remove much of this gunk accumulation since bleeding draws from the top of the bore. It would be interesting to see how much gunk remains in the bores after flushing if one was to pull the pistons.
I just tend to replace the brake fluid, hoses, calipers, wheel cylinders and master cylinder about every 10 years.