AFAIK CNs don't declare on CNs of your allies, other than that you're going to have this risk if you have them.
Edit:
I usually don't mind, as I can win the colonial wars and off the opposing CNs. The extra money and FL to merc up or spam buildings is nice to have. I don't like colonies as a big investment but once you set up a CN it'll take care of the coring on its own, eventually take expansion (due to the bug blocking them taking it on forming) and slowly colonize, and increasingly have a much larger army than anybody else that bothers to colonize land near it. CNs get a 3% missionary strength NI too so unless you're making a pagan CN they'll have no trouble converting captured provinces, and in 1.8 they seem to do it more consistently than before; both Brazil and La Plata for me as Songhai are almost 100% captured off Iberians, mostly foreign culture while I colonized Cape + other non-tropical stuff in Africa. Even the 7 tax type stuff is Sunni now. If you get a CN and a no diplo for provinces CB you can swap swathes of land to your CN, though of course you can just full annex to inherit AI CNs also.