Actually I appreciate the fact that all magazines have tracers at the end of them, from what I've heard and from my own experience it is really useful to do this in real life so that you get notificated in case you have to reload. However it is definitely a problem in case of covert operations due to the simple fact that the enemies can see your own tracers as well, a silencer is nearly useless if the enemy can see your bullets.
My suggestions in this case:
Either add another kind of mags that have no tracers in them.(the uncomplicated way)
Add another kind of magazines without tracers and rename the current mixed mags to something like "tracers mixed".(the kind of uncomplicated way)