Best graph for missing data
You are approaching the question from the wrong angle. In essence, you assume that there are canonical ways to show particular data. But that's not true. In the beginning, there is just data, i.e., raw numbers. Then, as the author of an article/thesis/book, you want to use this data as a way to illustrate a point you're making, and the way you show the data is chosen in such a way to make this point in a way that makes it easiest for a reader to understand what it is you're trying to explain. What this way to show the data is depends crucially on what you're trying to explain.

To give an example:


If you have rainfall data from each month (January to December) from 2000 to 2019 with two months every year missing (meteorologist is on vacation every year in July and August), and you want to illustrate which months form the rainy season, then maybe a bar chart would be appropriate where each bar indicates the average for that month over the years. In that case, there would simply be no bars at all for the missing months. If your bars start at 0 mm rain per month, then missing bars can be obtained by just using zero data, though it's still useful to indicate the missing data in the text or the caption.
If, on the other hand, you have the same data set and your goal is to illustrate inter-annual variability, then you can't show averages and it's also not useful to show a plot with 12x20=240 bars because you want people to see how different the 20 years' January rainfall is. In that case, you probably want to again show a plot with 12 x-values (one for each month), and each year's data would result in one point that you might want to connect to the previous and following month's data point by a thin line. This way, you'd overlay 20 curves in the same graph. Again, the missing months would not have any data points, and I'd probably also not plot any lines between the June data point and the September data point to make clear that there really is no information.


The point I'm trying to make here is that one can not answer the question of what the best way to show data is, unless we know what it is you're trying to say with your graphics.