As far as I know, most researchers use general drawing tools to visualizes neural network architectures. Although there are some libraries to do it automatically. However, the visualizations in your paper are quite important to get your ideas across and using custom hand-made visuals allows you to visually explain your work in the most appropriate way (not being limited to the design choices of an automated drawing library).
Therefore, I suggest to just use a general drawing tool of your choice. Also, MS PowerPoint or Google Slides can be quite convenient to draw shapes as in above picture.