Defining efficiency of the intercooler as the drop in charge temperature that it provides against its drop in pressure - yes injecting water before the IC will decrease the efficiency with which it does its work.
However, we are not just looking for IC efficiency but total charge intercooling efficiency.
To the extent that injecting before the intercooler results in lower entry and still lower IC exit temperatures and increased densities this is a good thing even if the entrance to exit drop in temperature is decreased, the exit temperature is what is important.
As you said injecting before the IC also helps with heat soak both during staging or on road tracks where intercoolers can become interheaters.
Lastly injecting before the IC lengthens the induction path of the water spray - giving it more time to absorb heat and also more time to mix smoothly before the plenum.
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