These days you can get the most amazing humidor designs which are supposed to enable you to keep your cigars untainted during storage through the use of appropriate separate sections, thereby avoiding the mingling of aromas of cigars from different sources. In my opinion this is all somewhat of an exaggeration.
Provided that no flavoured cigars have been stored in the humidor (which should be avoided at all costs) I, at least, cannot tell from the smell whether a Honduran cigar has been stored next to a Cuban or Dominican one. Maybe a true sommelier would be able to detect a slight difference in nuance, but I cannot. And even if there should be some transfer of aroma between the cigars, this would have no noticeable effect upon the taste, since the aroma of a cigar when the tobacco burns is much more intense than the aromas you can detect from a cold cigar with the nose.
My conclusion: There is no reason why you should not store cigars from the most different origins alongside one another in the humidor. Flavoured cigars should always be stored separately (in a separate humidor) from Puros.