It depends on what you're putting in there. Hard objects tend to reflect sound better than soft objects. If you're putting a jacket in the trunk, you'll notice a little drop in bass, but if you put something like bricks in the trunk, you'll keep most of your bass.
Also keep this in mind: the size of your trunk and its reflectiveness to sound greatly affects the bass you hear while you're in the car. Putting a lot of cargo in the back will lower the amount of air in the trunk and change the fidelity of the bass a little.
So yeah, the sound of the bass depends on the material of the objects you're carrying and how big it is. But unless you're carrying a lot of stuff, you probably won't notice much.