Do you mean SEO with SE? One thing has nothing to do with the other. Make your PHP code to output SEO friendly HTML, then encrypt your PHP code. The result will be the same.
yup. but do you anysoftware that i can use to encrypt php code? for example i want to encrypt my wordpress theme footer links
Well there are encryption methods like ioncube and zend guard but these feels like an overkill just to protect footer links.
Zend Guard will require Zend Optimizer installed on all servers that use the wordpress theme. Ioncube can decode on the fly. Ioncube does have a online encoded edition that can be used if fairly cheaply if you just have one file to encode. But like InFloW said, seems like overkill just for the footer links.
Why have not you enable mod_rewrite on your wordpress installation? Or you mean it do not work for the footer links?
ioncube works pretty damn well. kept me from making some money because i couldn't modify what i needed to.