A factor of 1000 isn't that important.
Really. First, stare at this chart from the Ars Technica article:
http://cdn.arstechnica.net/wp-content/uploads/2012/08/expone...
This graph shows, roughly, that a short password can be brute forced in seconds using modern hardware. If it is just one character longer, it suddenly takes a week to brute-force. This is the miracle of exponential functions.
Now multiply the y axis by 1000. The long password now takes 1000 weeks. But the shorter one still only takes a few thousand seconds. If you are running your cracking program for a day, you'll get the same results you got before. The weak passwords are still weak enough to crack. The strong ones are still strong.
(Note, by the way, that it doesn't take 1000 times longer to guess 1000 salted passwords, because some of those passwords are super weak and will fall in seconds, after which one no longer needs to guess them. So, for example, once half the passwords have been broken, the new multiple is only 500. The Ars article explains this, but I didn't understand its wording at first.)
It is true that salt makes some difference. But it is not a meaningful difference. The difference between giving up 60% of your passwords and giving up 73% of your passwords is probably moot.
EDIT: And my example number of 73% is too low! That is bad news for MD5! Again, the article: they cracked 82% of a 16k-password file in one hour using only a single commodity GPU.