Humans come along thinking Gods design has no purpose 
I would be worried about dust and particles causing issues down the road. If the nostrils were supposed to be open the natural coverings wouldn't exist.
Most likely, the people that do this are using it to mark culls for sale, so they don't care about the long-term impact. I wouldn't give them any further business, whether they've talked you into the idea you're getting a "deal" or not.
	
		
	
	
		
		
			Preventions I do are mixing up a mosquito spray to spray all around my coops and pens, bug zappers, or traps for them and since most of my birds are in a large greenhouse type building we made for them I roll down sides at night so no mosquitoes can get in.
Supposedly once a chicken gets it they will then be immune. Its sort of like chicken pox.
		
		
	 
Since we're in FL we get fowl pox in the juveniles most every summer. Never in the adults who already had it, no matter how much they're exposed to it again.
It sounds like you have a good system in place to try to reduce transmission, but just know that unless the flock is kept behind the netting all mosquito season, you're likely to keep getting it. It's not your fault.
One distinction I wanted to make, just in case you haven't seen it, is that 
dry fowl pox (external) is a lot easier for them to recover from than 
wet fowl pox. That's when the virus spreads to the inside of nostils, mouths, eyes, throat, etc. That's the dangerous form... and the most likely way that it occurs is from the water source.
The chicken(s) come to drink and shed viral particles from any dry pox on their face... that then enters the water and when they drink the water can infect the mucous membranes. Some chickens can even die from that if they don't have a sufficient immune response, but in any case they will carry the wet version a lot longer.
So what I do all summer long is dump, rinse, and refill water stations once a day. If someone has noticeable pox I step it up to twice a day. It does help. Although it might be better - and less work - to find an antiviral for the water, but I don't yet know of any that are both effective and safe in that context. Some put iodine in the water but it doesn't kill the virus. It just helps dry out the pox sores, and is supposed to reduced the infective time period a 
little. I'm also wary of adding anything to the water at this time of year that could reduce their consumption rate, dehydration in this heat would not help them recover and it would impact all the birds at once. So I just keep the water as fresh as possible.