Ben, if you have an account at Pdfcrowd then the logo is not rendered when
- you create PDFs via the API, or
- you use the online conversion form.
PDFs created using http://pdfcrowd.com/url_to_pdf/ always include the logo. We will offer logo-less PDFs as a paid feature in the future.
As to fonts - please could you elaborate more on your problem? If you have some special fonts we support the CSS3 @font-face rule. Fonts specified using this rule should be downloaded and embedded into the created PDF.