Regarding diagrams ...

Frederic Marand (fgm) has done some of those
done in the past, albeit for 4.7:

http://blog.riff.org/2006_05_14_data_model_for_drupal_4_7_core

One for taxonomy (4.6)
http://blog.riff.org/2005_11_27_grokking_drupal_the_taxonomy_system

He also did one for ecommerce:
http://blog.riff.org/2006_10_07_grokking_drupal_ecommerce_dependencies

And project:
http://blog.riff.org/2006_07_28_grokking_drupal_the_project_module_in_drupal_4_7

As for a tool to generate diagrams (with some manual work), I had some success
with Open Office 2.2 Database which works fine with MySQL (haven't tried Kexi).