What is the best to way to include charts and graphs in a pdf file?
Depends on your tools, skills, and the kind of charts and graphs you want to include.
Can I create simple bar charts using xsl:fo or svg?
You can use XSLFO tables or rulers for simple bar charts, the same way you can in HTML. SVG actually allows not only simple bar charts but also fairly complex ones. You should start with simple charts, especially if you want to use XSLT for generating them.