Salmon farmers don't keep their stock long enough to care about potential long term health effects - from anything.
I have actually read comments from Discus keepers that state that Carophyll Pink does indeed cause long term health issues in fish, and many of these various dyes, lakes, and other petroleum (coal/Tar) based synthetic color enhancers are actually banned in may parts of the world, due to the human health risks that have been associated with them.
http://hubpages.com/hub/GUIDE-TO-ARTIFICIAL-FOOD-COLORINGS
As an example, due to the health risks associated with FD&C Red #40 (aka Allura Red AC), its use is currently banned in Denmark, Belgium, France, Germany, Austria, Switzerland, Sweden, and Norway....... yet this product is still being used by some fish food manufacturers. (at least 1 that's manufactured in the USA)
The reality is that MOST of the synthetic food dies (especially those used for the color RED) have at some level been associated with health risks in humans, and I can only imagine how they might potentially effect the health of a fish from long term use.
There was a big stink over this in the UK a few years back.
Salmon dye can damage eyesight of consumers.
http://www.thefreelibrary.com/Salmon+dye+can+damage+eyesight+of+consumers-a087749668
http://archive.food.gov.uk/maff/archive/food/fac/facnews/issue3/page2.htm
http://newsletter.vitalchoice.com/e_article001320312.cfm?x=b9bTHlf,b63lMhyt,w
