Is it true that php code, while it has a purpose to mask url's and e-mails from spam bots when you've managed to gain a link on anothers website, blocks your link on that website from google bots aswell? If so what is the point in gaining a link on a site that has the php coding on your html link if the google bots won't pick it up?
I'm assuming if the spam bots can't find them the google bots can't either.

Right, Google won't count them, at least not at the present time. Some people give links this way in order to keep from leaking PR to you and assume you won't know the difference, or because they really dont want to be seen 'endorsing" your site. Some do it because its easier, due to their CMS and/or because it is part of a click-counting mechanism and they are ignorant of a better way to do this. If the point of getting the link is because it's likely to deliver traffic to you then it should not matter, but if you are looking for links to gain rankings only, this kind of link is not going to help.

Make sure to check the server header responses and verify that there is not a 302 response being given. When dealing with tricky (or clueless) link partners this is a bigger danger than simply not getting the PR/anchor passed.

Okay thanks JohnW, that has solidified my thoughts on php. Hopefully one day soon google will be able to pick up on those links with that coding. Ranking is what concerns me, and links is a great way to get ranked as long as the sites you link from have your best interests in mind. Many have the php to count your 'hits' and this makes it difficult to gain link favour in google.
That has been my main concern.