You could try one of those mods that remove the visual effects without affecting any of the bonuses since you're on Pc. That should help if it is the visuals that are bothering you. Do you also lose all the gameplay bonuses like Rof, accuracy bonuses etc while HM is flickering on and off?
I came in here just to say this, damn you Sir TeaKrogan!
If the overlay is misbehaving, disable overlays, is simple fix, that I am jealous of. Most of the overlays give me headaches. Which is sad, because they all offer awesome bonuses.
I have done both with dropping hunter mode and rolled with the scanner...or vice versa with that gear slot...there is not a gigantic difference in damage output...It's all almost the same, depending how you spec for weapon / power damage along with adding all the amps. the only noticeable difference I ever saw, was the gimping of the shields with hunter mode....but even that can be worked around.
I use the BPP on my GE and my TSol. I can tell you beyond any doubt, the RoF bonus is VERY noticable. And almost ever gun benefits from the increased accuracy, as the bullet spread on most defies logic. HM isn't about the "Damage Bonus", or even the wallhax (Geth Scanner accomplishes this without sacrificing shields). Plain and simple, it's about the Weapon bonuses, unless some weird kind of Geth Vorcha Trooper that doesn't understand how amazing he is with guns, then it is about the Power Damage. And movement speed bonuses are also amazing.