I was wondering if complicated if/else structures in my PHP code could be a bad design decision. Does having a lot of if statements make PHP run slow, site load slower etc?<
Very complicated if/else structures indicate a bad design in most cases. You can better focus on improving a bad design than optimization, premature optimization is the root of all evil!.
If you give an example of the type of code you are talking about, it will maybe be possible to give a more detailed answer.