Very true, but it's all in the DESIGN.
If I may add one of my own ideas:
I have a fighter with 6-8 "drones" I can detach, These drones are updated with MY targeting info so if I shoot at something THEY shoot at it also. If I am destroyed they either lock on and kamikaze the closest enemy unit, or self-destruct.
The key in drone security is access and capability. The more your features are HARD CODED and changeable only on site and NOT via remote, the less you are able to penetrate it and hack it.
At best, if an enemy ever discovers the unique identifier for any ONE fighter and it's drones then if there is any "confusion" a drone can be programmed to self abort until the confusion is abated, or just self destruct.
Ideally this means the enemy can start neutralizing drone sets ONE at a time, but you will neer get them to turn on you. Now if you have an enemy unit broadcasting the EXACT base control IFF signal and destroy the actual controlling fighter THEn you might in theory take over that drone as it's new MASTER...
But in mass combat (and no real focused planning) do you think it would actually happen outside of a bad "sci-fi Channel" movie plot???
I seriously doubt it...

The WORSE thing you could ever do is have a base use mass remotes and have them all ont eh SAME FREQ. You are only begging someone with jamming or hacking knowledge to spank your arse with them...

No strategy, however brilliant, survives piss poor incompetent implementation (be it by actual or arm chair generals)...