As you can hear, when they are using 9 instead of 27, although it gives them lower minimums due to the ILS, it can create problems for departures because the length of usable runway is shorter. Thus there are weight restriction issues. (You hear on the recording many of the 733s indicating that they can not accept a 9 departure)
I don't think it is just that the runway would be shorter, because it really isn't.. The big problem would be the rate of climb when departing 9 instead of 27. Looking at both the BORDER5 and LNSAY2 charts, you're looking at a rate of climb of 610ft per NM to 1900 off of runway 9, compared to 310ft per NM to 400 off of runway 27. Yes, you'd need to use less of the runway for the climb out rate, but there you go..
BL.
EDIT: BTW, pt9 is absolutely right. VFR minimums are 3SM
and 1000ft ceiling. For some (stupid) reason, I had it in my head that it was OR, when it definitely is AND. So SAN was IMC at this time, making LOC27 hellish.