We're all naked here....
Like most cartoon anthropomorphic animals ponies tend to stroll around starkers already being covered in a coat of hair. When drawn with clothing it tends to follow the Donald Duck syndrome and cover only the top half.
I've noticed that when it comes to ponysizing or whatever established canon characters (as opposed to original characters) clothing and accessories are used more often then not.
Makes sense, anything that helps identify the character, well, helps.
That said I find it weird when they're drawn wearing pants. Maybe it's the years of watching Donald Duck sufferers, maybe it's because it would cover up the cutie mark, or maybe it's because putting the pants on would be an even bigger pain in the ass then getting the shirt on, never mind off.
I also find it weird when they are drawn wearing trousers.
-----------Click to view the other My Little Time Lord comics done at the same time as this on Tumblr.
----------- More Pony art