Mud appears when you have 1/7 water evaporating. However, where is no water, there could be designation to dust mud away by Dwarves.
Currently to deconstruct floor takes a very long time in comparison to construct floor and what is understandable deconstruction process takes longer then construction.
Currently construction/deconstruction is the only way to clean mud, blood and so on from places Dwarves won't bother to or can't be ordered to clean.
This makes cleaning inside constructed on surface buildings more hazardous as well. Dwarves sometimes manage to stand on floor, which they are deconstructing. Doh!
Dwarves do clean walls under ground. Sometimes.
What is not happening on surface is magic of rain. Landing rain drops do not splash in 9 tiles area, like the cleaning work performed by Dwarves. Currently rain looks more like dry blue sun-rays burning surface clean, then wetting and watering it. Also announcement "it rains!" creates instantly a vast sea of blood pools on surface, which rarely gets cleaned entirely, before it stops "ray-raining".
Also, what is disturbing blood pools tend to "hang in air". Usually 1 tile above ramp or there where tree top was, before it got chopped down. Sometimes animals do get killed by hunters while hiding in the treetops. The burning of rain-rays does not burn away those air hovering blood pools.