it depends on 2 things:
- how powerful the tracking service / program / script that the advertiser (or you, depending on who has access to that script) uses is, and what data it logs (most tracking services on the market today log more information than you know what to do with, so in this regard everything should be good)
- whether or not you (or whoever places the affiliate link on pages) cloak and / or redirect the URL. I'm not very knowledgeable on how cloaking and redirections work and how they happen, but I know for sure that one of these 2 is responsible for the full or partial displaying of the links.
So, if you don't cloak and you don't use redirections, whoever clicks on the affiliate link will be able to see 100% the entire URL (including the affiliate code). If cloaking and / or redirections are used... well, it depends on how well the affiliate links are cloaked or redirected I guess