I have discussed long ago (in the Panic in the Woods thread) a theory of mine that humans take up a certain amount of psychological space. When we are in a space too large for the number of people in it, we feel too alone and, therefore, nervous. A school is normally crammed full - frequently too full - of people, so that every square inch of it is under control. When they are empty, naturally they feel wrong. Also, the acoustics almost universally suck, creating echoes and peculiar sound effects that increase the feeling of empty space. Schools that have creepy or "haunted" space - a janitor's closet where someone supposedly hung himself, steam tunnels where LARPers are rumored to have gone mad, a Hellmouth in the basement - keep them in places where no one goes, an unnatural state for any part of a school.
My own house has plenty of peeling paint and deferred maintenance, because we hardly ever have both time and money to deal with the contractors and/or mending chores until a problem becomes acute. You have to ride contractors all the time, especially in a sturdy old historic house where if it's not done right it's better not to do it at all. (Believe me, we're living with the results of shortcutting and grafting modern techniques onto an old structure, and we don't want to waste money making it worse!). I'm sure the neighborhood kids regard us as haunted, though the little girl next door - who went out of her way to introduce me to her kitten - doesn't seem to regard me as a witch. But unless you're alone in the house after dark, it's a secure, homey-feeling place. People who come inside don't appear to notice the deferred maintenance much, even though some of it is appallingly visible.
So I think we may notice deferred maintenance more on abandoned houses, whether it's really worse than the inhabited house next door or not.
Also, the practice of boarding up windows to prevent people throwing rocks for them automatically makes a building look decrepit.