The law actually reads "..using no more than 10 of the following..." So the law is really only concered with the total number of foregin parts in the gun. Most folks just use the "you need six parts, ect" as an easy way to explain it. If you put the "X" amount of parts in, then you will have less than the 11 ("no more than 10") foregin parts.
When you take the mag out of your gun, you're removing three parts out of the equation totally. It's not the total number of US parts, i.e. "you need six". It's the total number of imported parts in the gun, i.e. "you can have no more than 10". If you removed the mag and never used it (not much fun, but you could), you would be removing three foregin parts from the gun right there. It doesn't matter if there's US parts in the mags or not, those three parts no longer matter towards your parts count.
So the short answer is you are perfectly legal taking the mag out. As long as you have "no more than 10" of the listed foregin parts, regardless of if there's a mag or not, you're OK.
Ross