I have several coolerdors and smoking humi's. I do not smoke or have any of the flavored cigars out there.
In my smoking humi's, I usually have 5 to 20 different kinds of cigars in there and some for as long as 2 to 3 years. I usually try to keep the darker wrappers apart from the lighter wrappers and the milder smokes apart from the stronger smokes. By apart, I mean not touching but in the same humidor. Unfortunately, this approach is not always possible.
I have found that there can easily be changes in the pre-light scents/aromas of the cigars due to the different kinds stored unboxed and nude in the same humidor. However, once lit I have never seen any effect of "marrying" or whatever between different cigar types. When I keep the cello on, it seems to prevent or resist effects with pre-light scents/aromas.
Keep in mind that I have only kept or aged cigars for a few years at most, so very long term the effects may become more obvious. In any event, I have a 100-ct humidor where I only keep assorted singles and doubles. The aroma on opening the humidor is so delicious I am usually tempted to stand there and sniff for a few minutes.
Hope this helps,
antaean