The Dynkin diagrams of type ADE are ubiquitous in mathematics as solutions of various classification problems. The diagram E6 is usually drawn by five dots in a row with a sixth dot above the third, see for example here. There would be many other ways to draw the diagram E6, for example the sixth dot below the five dots, or just a capital
E.
Is there a reason for drawing that diagram in that particular shape beside or is that just a confirmed habit?
The question as stated is not really helpful, but it's worth pointing out that the ADE and other graphs/diagrams evolved over a couple of decades in different countries. The graphs, which encode at first the Coxeter data for finite (or more general) reflection groups, go back at least to Coxeter's 1934 paper. In Witt's 1941 paper these now familiar graphs reappear when the reflection groups are unified with the classification of root systems for semisimple Lie algebras over $\mathbb{C}$. Here the vertices correspond to simple roots, not just simple reflections, so the notation has to incorporate some length information. Dynkin's fundamental 1952 papers used the resulting "Dynkin diagrams" with extra labels 0, 1, 2 at vertices to classify efficiently the nilpotent orbits. Along the way a number of different choices were made about adding edges and arrows or making some vertices darker to distinguish lengths. Bourbaki's 1968 treatise is by now the easiest standard source to follow.
The graph itself is drawn in a typographically convenient way and can vary as Scott notes (note especially Coxeter's type E pictures). An even more arbitrary convention governs the numbering of vertices or simple roots. Here again the evolved version in Bourbaki is well established, though some authors like Carter depart a bit from that numbering. The history of ideas is quite interesting, but at the end of the day a convention is just a convention.
I disagree with the universality of your question, but I agree that the diagrams are often drawn in similar ways. They are drawn that way because they are easy to draw that way, and there isn't a good reason to deviate from what we are taught. I have seen both of your proposed alternatives for the $E_6$ diagram in the literature, and I might even say that your first alternative is the most common drawing I've seen.
There are in fact alternative conventions, e.g., if you put a 120 degree angle between consecutive edges, you don't have to spend as much time drawing vertices, and this can be helpful if you have to draw a lot of them, or have difficulty drawing convincing dots. As Guntram noted in the comments, some Wikipedia contributor has found a clever way to compress all of the Dynkin diagrams into a small, unreadable box.
