I don't believe this is the case (valves stop working). I put an inline on/off valve on the outlet hose for some testing- to see if it makes a difference. It really didn't make a noticeable difference. There are several threads regarding blocking this off for different performance characteristics. See link below, or pasted text. There are more like this.
http://www.snowest.com/forum/showthread.php?t=177443
8) Plug the exhaust purge hoses coming off the exhaust valves, this makes it like the 2001-2004 set-ups and definitely improves acceleration by allowing the exhaust valves to open sooner. An added benefit is the hot exhaust that was "held back" in the engine is released sooner, thereby effectively reducing internal engine temps.