It will definately affect them in a negative way. Deer use their ears and nose the most of all their senses. If they hear/smell coyotes close, they'll be outta there fast. BUt if they hear coyotes off in the distance they will be more likely to stay put and keep their guard up. If I were you, I would shoot any coyotes that you can. They are getting thick around my area here in north central MO.
...and on that day when my strength is failing, the end draws near and my times has come, still my soul will sing Your praise unending, ten thousand years and then forevermore!