Would is employed as it is in conditional constructions, to imply unreality. There is no explicit condition expressed, but sentences like this imply either a condition which is supplied by the context or what you might call a "universal condition" (don't quote that, it's a term I just made up):
EXPLICIT CONDITIONAL: Under these circumstances we would do such-and-such.
IMPLICIT CONDITIONAL: [Under the circumstances previously mentioned] we would do such-and-such.
UNIVERSAL CONDITIONAL: [Under any circumstances] we would do such-and-such.
Certainly modifies the entire sentence, thus emphasizing the negation which is its core. It might equally be written:
Certainly, we would not advise you to approach the site yourself.
We would certainly not advise you to approach the site yourself.
So what the sentence amounts to is either:
IMPLICIT CONDITIONAL: It is certain that [under the present circumstances] we would not advise you to approach the site yourself.
OR
UNIVERSAL CONDITIONAL: It is certain that there is no circumstance under which we would advise you to approach the site yourself.