The way that my native Korean speaking friend explains it was that 것 replaces the noun, since we explicitly say desk, 이 is fine. As for no 은, the topic/subject marker comes after the desk as that is what we are talking about.
책상 ends in a consonant so you must use 이 to make 책상이. Words ending in a vowel can use 가 such as 사과 -> 사과가.
는/은 would be used to mark the topic and 이/가 is used for the subject.