Similar case for my user with OS X Yosemite and 9.0.1FP4 IF1 RU_PL (32bit version) - text in messages (new and recieved) is not displayed partially or completely. Restart client can help in some cases. I need help too...

If the issue is consistent across client restarts - check to see if the user has changes their default Fonts - File -> Preferences -> Basic Notes Client Configuration -> Default Fonts.

This has happened here a time or two in the distant past....

Me and a coworker tried to tackle things again today

Issues only occur when the user gets mail from an external source (we used gmail.com). all fonts came back normal except for sans-serif. internal mail works fine for sans-serif. also, when forwarding the problem message to another person, the text appears fine in the new window. As far as system fonts go i copied my fonts to his mac so we have the same and the issue still persists. 

The tiny fonts issue on MIME email has been around for several releases. The cases I am familiar with involved a lengthy thread. It was the later exchanges that became affected. If I opened the problem message from another PC, I would not see the tiny fonts. Running NICE on the user's PC, and reinstalling Notes would address the problem.