She knew. If you recall, Locke took off from camp in the first season, after he had encountered Smokey and "looked into the eye of the Island," and someone....Boone, I think...followed him and wanted to go along. He told him that he should turn back, especially since it was getting ready to rain. Boone told him that it didn't look like rain, and a few seconds later it started to pour down. I think Boone said something like "So, they teach you that at the box company?"
Juliet, like Locke, has a connection with the Island. I think part of this connection is being in tune with the weather.