Can someone tell me why most piping diamgrams show drilled holes in bolted flanges straddling the vertical centerline, so as to not have a hole at top dead center?

In addition to the wise and appropriate answers you have already gotten I will give you two others.

1 - You will find that with the bolts on the vertical centerline there would be a problem with getting a wrench on the nut on some valves.
2 - Many valves/Forged Steel Valves, both cast and forged have a reinforcement "Web" right at the "12 O'Clock" position connecting the back of the flange and the rest of the valve body so a bolt hole is out of the question.

I too would like to add one more answer to the already "wise" answers you have already received. When welders