What do you mean by <href>? Links should be site-absolute:
<a href = "/directory/innerdirectory/page.html">
We can argue about whether relative links
<a href = "otherpage.html">
are appropriate when you have a group of pages that will always live in the same directory.
afaik search engines don't care, because they never follow a link directly. They translate it into a complete URL including protocol and domain, and put it on their shopping list for later.