Government Man's Guide to San Diego Hotels 
(with updates)
Part V: Hotels Near Trolley Stops: The Run to the Border
We will now turn to our final option if we're using the trolley: the Blue Line running from Downtown to San Ysidro on the Mexican border. This isn't going to be pretty, folks.
Blue Line Stations (San Diego)
Barrio Logan
The fare to the Convention Center is $2.00.
28. Americas Best Value Inn Convention Center/Downtown (0.25 mi) *
$266
Skip two stations.
Blue Line Stations (National City)
8th Street Station
The fare is $2.25.
39. Howard Johnson Express Inn National City (0.46 mi) ** 2D
SOLD OUT on Expedia!
Skip one station.
Blue Line Stations (Chula Vista)
Bayfront/E Street Station
The fare is $2.25.
40. Good Nite Inn Chula Vista (0.10 mi) **
$135 225 Bay Blvd, Chula Vista 91910
41. Best Western South Bay Inn (0.14 mi) *** 3D
$88 710 E St, Chula Vista 91910
41 (again). Days Inn San Diego / South Bay (0.16 mi) ** 2D
SOLD OUT on Expedia!
42. Vagabond Inn Chula Vista (0.41 mi) ** 2D
$125 230 Broadway, Chula Vista 91910
Skip to the end of the line.
Blue Line Stations (San Ysidro)
San Ysidro Transit Center
The fare is $2.50.
43. Travelodge San Ysidro (0.16 mi) **
SOLD OUT on Expedia!
And that's it.
34 of the original 50 hotels are available (plus 2 new ones), 26 of them under $200 a night.
Hopefully, you should be able to find someplace to stay from that, but considering that 16 hotels became unavailable in a little over a month, you had better make your reservations as soon as possible.