Would your average EJ 2.5i driver notice a difference? I doubt it.
Would it effect your ABS/VSA module in the long term? Hard to say.
Dirt should stay in the lowest point of the caliper bores, just like it has since the inception of disk brakes. Regardless of what people say, fluid does not circulate through the system. It's not like there's a 'return line' from each caliper, back to the reservoir, etc. The crud that collects in the caliper bores does not get sucked back up into the system. You'd physically have to force it back up.
Hondas call for the same thing. Probably less than 1 in 10 people do it and I know my Honda dealer never pushes it. I'm thinking about doing it on our 2008 Odyssey given I'm currently at ~54K miles. All I've done to it is new pads all the way around and replaced some torn caliper pin boots I tore in the process.