The aftermarket pipes should have no bearing what-so-ever on your clutch recall. It's a recall. IF for some reason your pipes are more time consuming to remove/loosen than the stock units they may charge you extra for that...
When it comes to mods and what can void your warranty, there is the Magnuson-Moss Warranty Act of 1975. Which basically states the dealership has to prove the mod has caused the problem you are experience necessitating repair. For example you put open pipes on your bike and don't tune the air/fuel mixture and you burn your valves, they would have to prove the lack of tuning caused the issue. Now it may not be as easy as it sounds. A lot of dealers will put up a fight and it can take months to resolve.