Because they are two different words Nepali Language has totally different meaning for those two words: for example: कसको: whose: eg. whose book is this? यो किताब कसको हो ? कस्तो: how: eg. how are you? तिमी लाई कस्तो छ ?

it depend on pronounciation....

I think because ko, the modifier on kasko कसको is really more like its own word in some ways. Ko, implies a level of ownership, in this case, whose, like who owns. Kasto कस्तो , is a word meaning, how many, there is no ownership. You will see ko modify many things to imply ownership, but to at the end of kasto can not take its own meaning when attached to different words.

well sir.. when u pronounce "कसको " u will realized tht "s" is pronounce longer time then "कस्तो "...thts y there is full s in कसको :)