Find all pdf links using a module
It depends how the links have been created.

If the links were added using a field, eg using the file module, then you could look to that module for it's theme functions, and create your own replacement theme function in your module or theme.

If (just reread your question) the links are included in the body (or other textarea field) of your site's nodes, then you would have to rely on an input filter to alter them before displaying the field. You could look to a module like ELF, for how this can be accomplished using an input filter, or 'External Links' for an example using javascript.