That is not true. The vaccines get tested extensively before being FDA approved. However, there is nothing like real world use because they just can't perform tests on thousands of horses in a study. They must take a representative sampling and they aren't going to end up with one of every horse with every known medical issue in these studies.
And I am not saying your vet is wrong but showing you where reliable sources have stated that the vaccines are highly effective, including study results.
"Recent literature indicates that all licensed vaccines demonstrate approximately 95% efficacy when horses undergo intrathecal challenge 28 days post-vaccination. These studies support the epidemiological studies that have demonstrated high efficacy for vaccination. Thus vaccination for West Nile virus is recommended as a core vaccine and is an essential standard of care for all horses in North America."--West Nile Virus - AAEP
Equine Vet J. 2007 Nov;39(6):491-7.
Efficacy, duration, and onset of immunogenicity of a West Nile virus vaccine, live Flavivirus chimera, in horses with a clinical disease challenge model.
College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida, USA. Efficacy, duration, and onset of immunogenicity of... [Equine Vet J. 2007] - PubMed result
Vet Res. 2007 Jan-Feb;38(1):109-16.
Incidence and effects of West Nile virus infection in vaccinated and unvaccinated horses in California Gardner IA
, Wong SJ
, Ferraro GL
, Balasuriya UB
, Hullinger PJ
, Wilson WD
, Shi PY
, MacLachlan NJ
Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
A prospective cohort study was used to estimate the incidence of West Nile virus (WNV) infection in a group of unvaccinated horses (n = 37) in California and compare the effects of natural WNV infection in these unvaccinated horses to a group of co-mingled vaccinated horses (n = 155). Horses initially were vaccinated with either inactivated whole virus (n = 87) or canarypox recombinant (n = 68) WNV vaccines during 2003 or 2004, prior to emergence of WNV in the region. Unvaccinated horses were serologically tested for antibodies to WNV by microsphere immunoassay incorporating recombinant WNV E protein (rE MIA) in December 2003, December 2004, and every two months thereafter until November 2005. Clinical neurologic disease attributable to WNV infection (West Nile disease (WND)) developed in 2 (5.4%) of 37 unvaccinated horses and in 0 of 155 vaccinated horses.
One affected horse died. Twenty one (67.7%) of 31 unvaccinated horses that were seronegative to WNV in December, 2004 seroconverted to WNV before the end of the study in November, 2005. Findings from the study indicate that currently-available commercial vaccines are effective in preventing WND and their use is financially justified because clinical disease only occurred in unvaccinated horses and the mean cost of each clinical case of WND was approximately 45 times the cost of a 2-dose WNV vaccination program."--http://www.ncbi.nlm.nih.gov/pubmed/17274156
There are many many studies on safety and efficacy of these vaccines.