What effect have bay leaves in a meat/tomato sauce?
It doesn't do anything, it's your second suggestion. 

The feeling of "right/wrong" and "like/dislike" is highly correlated with familiarity. This is proven not only by psychometry, but even physiologically, with fMRI scans. People like most whatever they are familiar with, up to the point that unfamiliar things seem wrong. This applies not only to bay leaves, but also to all other tastes (or taste combinations) and many other areas of life, even beyond sensory perception. 

You can teach yourself to like bay-leaf-less sauce too, by just eating it frequently enough that it becomes familiar. But I don't see any advantages in doing so. Just cook with bay leaf and enjoy it.