Draft Issue?

I have two flues in my chimney; one for the fireplace and one for the boiler. I have a chimney cap on the fireplace flue but never put one on the boiler flue (I just have a metal screen over it to keep critters out). I've decided I should get a cap for the boiler flue to keep the rain out but while researching round chimney caps (it's a 10" diameter clay flue), I've read some talk about draft issues with chimney caps. Is this something I need to worry about with the boiler flue?
Thanks!!