Hmmm. . . I have 2 modern diesels and both have horizontal mufflers.
I don't think there is any real answer to the question. And I don't think there is any correlation between type of fuel and type of exhaust design. I think the main reason is to make sure the fumes do not hit the operator any more than they need to. So some tractors use a vertical stack to put the exhaust OVER the operator while other tractors use a horizontal exhaust to get it UNDER the operator. Another factor, tractors used in tall crops (like corn) typically have vertical exhausts or somewhat shelterd exhausts, that is probably so the exhaust does not start a fire. That is not much issue for most small diesel tractors, and most of those have horizontal exhausts.