Here my personal experience writing my thesis: Using one (serif) font in the text, pictures and charts seems to be the most elegant choice. However, using sans serif in diagrams, plots, figures, ... looks more technical and can be better legible. (all as you already mentioned)
I actually wanted to make the text of the captions of the figures and tables to be easily distinguishable from the main text. So I used a sans serif font for all tables and figures including their captions with one step smaller font size (\small
). I made sure that all sans serif elements have the same font size. I also adjusted the leading to give similar blackness levels on the paper for the serif main text and the sans serif captions. Robert Bringhurst used a similar approach in his typography book.
One possible issue: If the sans serif font has less font features (e.g. small caps) then the serif font, one has to find a compromise...
Even if you can only adjust the figure's font, the technical, more clear appearance seems preferable to me.
elsarticle
template is a typical example. I use bar-charts and have labels both within the bars and at the ends. I also use line charts and sometimes label particular points. I also use quite a few flow charts, and these are particularly tricky. They can use a lot of text, so continuity with the body text is important. But they can also be intricate, so small font size/legibility are important.pgfplots
for virtually all my plots and TikZ for my figures in IEEE and Elsevier articles. Hence the fonts are inherited from the text surrounding them.