I really don't see the point of replacing the screen element vs. just cleaning it honestly. I can't say we do it regularly though; most of the the failed transmissions I have replaced or had the pan off to inspect didn't have horribly clogged filters to the point that it restricts flow significantly.
I don't think Toyota has really used a paper style transmission filter in their transmissions for a while, almost all the ones I've seen have been a fine mesh screen. You can usually remove them and spray them out with brake clean and blow them clean, though as I mentioned I haven't seen any really badly clogged before.
You'll always see a lot of gunk on the magnets, even on a new properly operating transmission; so don't get too freaked out when you drop the pan. But make sure the magnets go back in the same spots they were in and that when you torque the pan back on you try to "criss-cross" your tightening pattern, it will help the pan seat more evenly and hopefully not leak.
Post Note-
I'm still hesitant to recommend anything other than the factory fluid, a lot of companies like to say "certified by Toyota or Asin" but, there's no real proof of said certifications nor do I recall seeing any documentation from Toyota regarding approved/certified WS alternatives (if you do have that document I'd love it for my own reference!). Also have never seen a definitive breakdown of what their additive packages vs. what WS additive packages are (hell I still can't find a definitive breakdown of what exactly WS is made of and what additives it has in it). My cautious skepticism aside, WS ATF has been around long enough that I would imagine companies like Amsoil, Valvoline, and Idemitsu could have made fluids comparable enough to it and plenty of people have beta-tested it for them, so I'm a little less knee-jerk about people wanting to use them than I was years ago; though I still stand by if you don't know what it is, you probably can't tell what to swap it out with.