I think you're exaggerating when you say you see "a lot" of these spaces. There are some. And they're usually vacant for a reason that involves money. Or there's a more serious problem (like contamination).

For example, the reason that space at 18th and Mission was vacant is right there in the article you linked -- the landlord pushed out the previous tenant, and turning it into a grocery store required extensive renovation. It's not as if the space was sitting empty because nobody had a use for it:

"So when the 99-cent store closed — because of high rent, according to neighboring businesses — and the vacant building went on the market in May 2010, he seized the opportunity and bought it two months later."

But yeah, it would have been nice if the new owner allowed someone else use the space while waiting for his redevelopment plans to go through, instead of letting squatters turn it into a drug house.