Using add archive when creating an OMOD will not ask you which of the same file you want to use, if more than one copy is present in the list.
Example:
data/textures/aaa.dds is already present on the list, and you use add archive to add another copy of data/textures/aaa.dds then create your omod.
OBMM will proceed as normal, and seemingly neither copy of the file in question will be installed.
When activating said omod, you will receive an error saying that the file could not be found in the temp folder, and omod installation will cancel.
On a [somewhat] unrelated note, editing and recreating the omod will allow you to install it normally. I'm not sure what happens to the file(s) when you do this. I assume they're just removed from the list. The user is not warned of any of this, either.