The blanking must occur around the state changes of the shift register outputs. It is related to the latch pulse, not the clock pulse (but clock pulses may appear by chance near enough to the latching to work, don't know your system).
So from HW side alone, you'd want to delay the latch pulse by some us, and blank the display around the latch pulse. If you route the OE pin to the controller, this could be a simple job for the SW guy, depends on the way things were done in the SW.
Blanking by shifting zeros into the registers is a bad idea, since this consumes a lot of time that reduces the brightness indeed, not necessarily by half, also depends on the way things were done in the SW.
In general it's a good idea to let the SW guy explain you how it is done, show him your problem (maybe point out increases component cost) and talk him into discovering the SW way is the better way to solve the problem. You may want to provide him the GPIO pin routed to the shift registers OE, that would be my choice to solve this issue.