opposite facing subs
 

Let's say you have one sub facing away from the cabin, right up against the trunk, and the other aiming towards the cabin.





Will there be cancellation or a coupling effect?

Yes, but not so you'd know it.



At sub-bass frequencies you're talking more about pressurizing the car than about wavelengths cancelling. There isn't enough room for a car to develop a standing wave (or even a 1/4 wave) so you can get away with just about any orientation for the drivers. The only way you might notice (maybe but probably not) is if they were in an especially acoustically efficient or deficient configuration. Almost any configuration that isn't ridiculous to look at, will probably be fine.