I have always heard that they are bad to use in aquariums, I have no data to back this up though. All I know is that I'm not willing to risk it in my tanks, it's too easy to just use pvc and not have to worry about it. For all I know it may be fine and never hurt a thing, it just isn't worth the risk to me.
As for our water coming through copper lines that is true, however it goes through it once and it is finished. If we have it in our systems then it goes through it over and over again. Again, it may not hurt anything but why risk it?