Like other insects, I believe flies orient themselves with light. Striped surfaces like this would cause some confusion with that. There's a few studies around about flight paths and light/surfaces around, if there's any interest I'll do a rummage. Light reflects, black absorbs remember. Very good for controlled contrast.

If you paint a black cow black, and it gets bit less, that would sort of give it away wouldnt it?

They already did sorta do that. One of the three groups was painted black on black, albeit with stripes. Those were bitten as much as the unpainted black cows.

To take it to the furthest conclusion I'd paint them entirely in black, and entirely in white (in case there's something different between the white and black paint besides the color).

The treatments were black-and-white painted stripes, black painted stripes, and no stripes (all-black body surface). Recorded fly-repelling behaviors were head throw, ear beat, leg stamp, skin twitch, and tail flick. Photo images of the right side of each cow were taken using a commercial digital camera after every observation and biting flies on the body and each leg were counted from the photo images. Here we show that the numbers of biting flies on Japanese Black cows painted with black-and-white stripes were significantly lower than those on non-painted cows and cows painted only with black stripes

The study says that zebra markings repels flies.