At first I found these ******* difficult with their turrets, specially on an 'open' map, as my gals got mowed down before getting anywhere near it. Even panzerfausts and the law-type handhelds took a few shots to get it. Now I'm up to tactical armour and juggernaut suits and have picked-up some UAC rocket-launchers, so it's rather easier.
I'm using a Fortuna, so I have a one or two gals in juggernaut suits with rocket-launchers at the top hatch, who pop-up and usually one-shot the turret. Then it's just a matter of the rest of them, with lasers and rail-rifles, mopping-up the remaining ninjas. In the bigger transporter there's always one hiding in a room with seagull missiles who can sometimes suicide herself - and take-out one or two of my gals - by 'accidentally' blowing-up the missiles! I even did that myself one or twice before I cottoned on to it! Take her out with melee weapons to be on the safe-side. Always try and make sure to knock-out the engineer guy though as interrogating him can be very helpful.
I'm playing on 6.0.7, and I haven't seen any larger Ninja craft than the crawler and transporter yet. There must be base somewhere in North Africa, but even having zeppelins hovering over the area hasn't located it.
