I think it all depends on context.
If John discovers life on Mars, he will be famous.
If John discovers that Mary is in New York, he will be mad.
Grammatically these two sentences may be the same, but contextually I think their meanings are very different.
Certainly the first does not imply anything about whether there actually is life on Mars or not. The sentence works either way.
The second sentence, on the other hand, does imply that the speaker believes Mary is in New York. Otherwise it just doesn't make sense to say it.
Whether Mary actually is in New York is a whole other matter :)
"If John discovers that Mary is in New York, he will be mad."
"Whatever do you mean? I just saw her five minutes ago!"