Whenever I have my wheel off, I always give the brake pads and the pistons a good clean. Push the pistons out a tad - as John says, until I can see the shiny surface - a wipe to remove the excess crud and then an old toothbrush and brake fluid. I finish off with the sewn hem of a cotton rag, wrapped around the piston and use a drying-my-back motion to clean it up.
When I put the wheel back in, I put the pads in temporarily and pump the pistons out. Then remove the pads and coat the exposed part of the piston with red rubber grease - a silicon compound designed for use on hydraulic seals. I find this to be much better here in the UK where we have lots of rain, often containing salt and water. Yes, the muck sticks to it, but it doesn't seem to get under the seals and the pistons always clean up nice and shiny.
I've only ever had to replace seals once - and that was on my first ST1100, which I bought at 29000 miles and it had been sitting around dirty for quite a long time. Then it took a good bit of time to get the crystals out of the seal grooves in the caliper with bits of sharpened wood and plastic card. The seals that came out were much larger than the piston bore grooves - clearly they had been exposed to petroleum based greases or fluids.
Having said that, my present ST1300 has some niggles. Nothing I can put my finger on, but something isn't quite as it should be. Brakes work fine and they seem to release perfectly OK, but the rear disk takes longer to cool down after the last application of the brakes than I think it should. So in the next few days, it is going to get overhauled. I have a new SMC, I have new seals. I'm just waiting for Santa to deliver my new Motorcycle ramp lift. That should arrive here before Friday. It niggles me because although it has done just under 40,000 miles and came off the production line in 2013, it is an A9 model (A9 was still the latest model in the UK in 2013), and I have no way of knowing how long the components were lying around before they were fitted to the bike.
So I'll report back here in a couple of weeks with what I find - the bike has been ridden in all weathers and all seasons.