I've noticed the same thing Xero. I also noticed that I have been burning through an enemy's Absorbers at a slightly higher rate than their Deflection bots when I use Shockwave, which surprises me considering the higher shield rating of Absorbers.
Now, given the description of Seekers, my impression is that they do attack through friendly Deflection bots, which must mean that leftover attack formations aren't actually fighting back until they start getting hit after the Deflection bots are gone. But GungHo describes it as if Seekers get the first strike. And if that's the case, how am I able to get through someone's Seekers at all? It seems like my attack formations should be wiped out before I actually get to the Deflection bots. I don't have many active enemies here, so my tests have been limited.