We, too, have a small vegan farm with chickens. And they help us with fertilizer and bugs. I consider the produce vegan. Actually, if I used synthetic fertilizer, I'd look at it the other way. Not 'is it vegan,' but 'is that vegetable safe?'
I wouldn't use manure from feed lots or synthetic fertilizer. Only what God made, preferably right from our own farm. But if you had a robust composting system, a small farm wouldn't need to add manure at all. There's documentary called "Back to Eden" about a novel idea of sustainable farming where the whole garden is essentially a multi-layered composting site. I don't believe he uses any fertilizer at all.
If the farm is using commercial fertilizer, it's probably not "vegan." There are some ethical concerns for sure. If I'm not mistaken, I believe there was eColi bacteria contamination of prepackaged salad from California due to upstream runoff from feedlot manure.
But some start wondering about the earthworms that composted the fertilizer - did they eat any dead mice in the pile and leave the castings? So I don't know if you need to buy certified vegan worms to put into the certified vegan compost pile to get the certified vegan fertilizer to make the certified vegan vegetables! :) Everyone draws the line somewhere.