I've got a set of +40 sneak boots vs the 'muffle' shrouded boots.
Which are more effective?

As far as my knowledge goes, 'muffled' boots is like sneaking barefoot, while boots with enhanced sneak increase your skill points but do not make you move quietly. So they could be better if the sneak points overpower the fact you will make noise, or worse if they don't.

Why don't you get the enchanting perk for two effects and have both?

Do you use the muffle spell or have the silence perk in sneak?

I have often wondered the same thing.

What does "muffled" constitute?
What kind of a bonus is that?
Is it better than 10% or 20% boost to sneak?, or not?

As far as I know there is no way to enchant "muffled". You only have the spell which can be cast.

Get a piece of jewelry with a sneaking enchantment and keep the muffled boots.