There is nothing wrong with having "Firing deploy hardpoints" on... the question more is why aren't you having 2 group assignments? KWS/wake scanner/cargo scanner and Interdictor/shield bank/ECM in a group and you always have that ready and only switch to the weapon group once in combat and you never have that problem.
I can't imagine any pilots will have enough primary/secondary slots with just 1 weapon group assignments, even if youa re just running a trade ship.