I generally remove as much brass first as is practical, as in my experience, Aquafortis tends to leave a whitish-yellow cast to the finish. But of course, some inlays and the nosecap are sometimes not possible to remove. In these cases, I just try and not let the Aquafortis sit on the brass very long, and wipe it immediately. All it takes though is a light burnishing afterwards to restore the brass to normal. Silver is another story... It will darken silver, and nickel-silver to, but in both cases, this is generally easily buffed away. Can't say about iron or steel, since I have never let it touch those parts. BTW, I am using TOTW Aquafortis, and not my own mix.
The main reason I remove the brass though is more that I tend to finish a gun under the parts as well, so it is not because of the Aquafortis I do it. I am just a believer in getting sealant of some sort on all parts of the wood that may come into contact with water.
Matt