hummm... I'm still trying to work out what you're up to! As I understand it, you have a multiple output Kontakt player open with 16 assigned outputs. These are then assigned to Logic Aux channels with the combined output of ALL of Logic's auxs going to the main output 1-2. Is this not overloading the output channel as it would do a bus, if you routed all of the drum outputs to the one channel? Are you running a multipressor/ limiter on your output at the moment? What other instruments do you have in the mix?
Depending on how you have Kontakt up, you could look at assigning all of Logic's Aux outputs (which has Kontakt channels as inputs) off to a stereo bus. This would then have the autofilter/ flanger/ effect of choice on. You could then automate the bypass of the plugin so that it effects the whole drum mix, but is only active when you have it out of bypass?
Another option would be to send levels from Logic's Aux channels to a stereo bus that has the effect on it. The sends could vary then just in case the effect you have in mind is more effective on certain drum elements than others (more snare less kick for example).
Or.... work with audio! Bounce the bits you want with or without processing and arrange that way!