All photometric information given in the Handbook assumes aperture photometry with a 0.5 arcsecond radius aperture (c.f. Holtzman, et al. 1995). Hence, total counts for a target (infinite aperture size) would be about 10% higher than obtained using the throughputs given in the Handbook. The difference is probably unimportant for SNR estimations, but could be important when calibrating observations.
This also holds for all previous versions of the WFPC2 Handbook, though it was never made explicit.