Not warts. Instead, normal; they're root initials.

If your plants are stunted, look for a different reason.

I don't know. I had the same problem with one of mine that is now doing well. It could be that the "bumps" are places that the tomato is getting ready to root from. This may be a characteristic of the variety,or not. It also may be an indication that there is a problem with the ground roots of the plant (root worm?) and that the plant is making plans to survive if it has to grow new roots. Sometimes a sick plant will sucker more vigorously as well, but I don't think that you can use this as an indication when growing tomatoes. I dried my plant out, pruned away the damaged leaves, or leaves too close to the ground and dosed it with epsom salts ( I figured " can't hurt "). The plant recovered.