I've taken two swims in waders over the years, one out west in a fast river gorge, another on a bayside tidal flat that flooded suddenly. Two things I can say are (1) you can't be too cautious and (2) it'll never happen again.
Horror stories I've heard and witnessed:
A guy popping up from a 50 yard underwater drift with only his underwear on after he dumped his driftboat - stating that if his suspenders didn't snap he'd be dead when his waders filled.
Bayside flats wader hanging on to a bouy until the tide changed.
Dead fisherman found with his waders pulled down to his ankles unable to get his waders off and hampered by the waders.
*probably not a good idea to try to take them off in the water!*
Pete's heroic rescue at Chatham Inlet.
In my humble opinion (in no sense do I claim to be nor want to be an expert in this!) the problem is not necessarily having waders on in the water, it's having waders that are full of water and having shoes that you can't swim in. If the waders remained watertight and the boots didn't keep you from making progress then it would probably help. Unfortunately the norm is that they fill up and big boots keep you from getting anywhere.
From a yak, I would think the #1 safety move would be stay with the yak. It probably wouldn't hurt to put a couple flares in the dry hold either if you are on the coast, cell phone is a real plus. GPS would make the event even less threatening, etc.
On shore, a few things I do for safety:
(a) CO2 pfd vest
(b) small roll of duct tape in my chestpack, enough to wrap tops of waders for three people thoroughly to slow or perhaps stop filling up. This only works on shore because you know the tide is coming and you have a moment to prepare.
(c) scuba style boots for flats - you can swim reasonably well in them
(d) compass, constantly take a bearing in fog or occluded vision - knowing where to go is half the battle
(e) whistle - approved designs that resist failure in water
(f) anal retentive on tidal flats on the incoming when on foot - know when to leave
(g) cell phone - watertight container needed
(h) will add a portable GPS this year
(i) use a proper branch or wading staff to wade in current, better yet don't wade where there is risk
(j) carbide studded felt soled boots in fast rivers, very rigid soles and support to prevent compression of the foot between stones
(k) most importantly avoid trouble situations and take safety very seriously
Most of those things are preventative, don't need to quote Ben Franklin there. Of the reactive measures, the pfd is without a doubt the best.
Like Adrian says, I've read the same about facing the feet downstream and trying to float to safety. That's exactly what they say to do when you are whitewater rafting and go overboard.
We've been lucky so far, knock on wood. Let's hope we never have to learn any such lessons the hard way!