I use both standard spds for mountain and a combo spd/flat pedal.

Why would some people use a combo? Mainly, you can stand on it without being clipped in. If you are doing anything technical, on a rocky trail, downhilling, or just need a broader comfort zone, it gives you more options than a regular SPD. Some people like them as an option in between true flats and a straight clip in. I keep mine on my "adventure" bike that I do small jumps, easy ladders and so on. I find that doing technical riding, sometimes that extra split second it takes to get clipped in can really mess up your timing.

I've never heard of them being a disadvantage in terms of getting whacked on things, but they do weigh more.

As for shoes, I've had the race style plastic soled shoes ( SIDI rampa) and have switched to a more skate/hiking type bike shoe. The main reason is those hard race plastic soles absolutely suck for hike-a-bike. If you are on rocks at all you will get no traction, and if you are on slickrock, you will go skittering and land on your ***. Ask me how I know this. I suppose if you are racing they'd be preferred,but I don't race.