1) Why are they there? I always "water deep", at least deep enough to get a good amount of run-off from the drainage holes.

2) Did I just kill my plant?

Why they are there ?: The answer is to get nutrients, water air. Tomato plan spreads roots in all directions.

Take a look at the link below, from 1927 and all the basic tratis of many different veggies and fruits were studied in the 20's and 30's, scroll down to the tomato chapter, look at the illustrations and see that fibrous roots grow outwards from the top part of the root to often up to 6 ft below.

The difference in a fibrous root and a tap root structure for tomatoes is if one direct seeds tomato seeds and doesn't transplanted them just once that one gets a tap root structure and transplanting them just once gives a fibrous root structure which is more desirable for water and nutrient uptake, but is more fragile than a tap root, which is why I always let my transplanted seedlings get rootbound before they were hardened off and put outside.

Fragile roots break easily whereas root bound ones don't, and take off ASAP to form a fibrous structure/ And I never, but never transplanted seedlings more than once, as in no, for potting up as many call it.

Carolyn