If a vehicle had been used to transport the girls there could be an article of clothing, an earring or a shoe, blood evidence or hair. If it was used to transport a dead body it would stink by now, even if just a small amount of body fluid was left. ( Remember Casey Anthony's trunk?)
I think that stopping vehicles to check trunks could also be a good excuse to observe the demeanor of the people in the vehicle. Someone who is overly anxious could be hiding guilty knowledge. Perps are known for finding ways to be close to the investigation, so it's a good idea to know who is hanging around, watching LE.
I thought the trunk reeked because Kaylee actually decomposed in the trunk for days not was killed then removed quickly. I also thought only dogs could smell decomp that happens within minutes of death because of their keen sense of smell.