I live in an area where there is a lot of mud. I mean, a LOT. The soil is blue clay and the water just sits on top of it, even if there hasn't been good rainfall for days/weeks. It simply doesn't drain because there's nowhere for it to go.
I don't put any leg protection on my horse when I ride the trails. I figure it's more likely to get bogged down with heavy wet mud, or torn or caught up in underbrush.
But, if this is a new horse and you're not sure how he'll do on different terrain, I don't think there's any harm in trying him in some leg protection first. As you go along, you may or may not decide to continue using it.
"Parelli horsemanship is just like painting by the numbers. You need absolutely no skill. You just put this color here and this color there, and when you're done, you have ... a mess no one wants." mp