Yes, if they're looking in your direction and within the view distance, which is 40 with the latest update, they'll spot you. They won't be able to shoot though until they can spot you on their turn, but they'll remember where your gals are, and may start hunting them more aggressively.
On a related note, I've found that reloading a save turns the lights back on even when they were off when you saved, so be careful about needing to come back to a night op you had to leave partway through. Also, the Pachyderm is terrible for disembarking at night; even when personal lights are off, the engines are a beacon declaring 'Yarr! Here there be piratez!'