Sometimes a flower is just a flower, but sometimes the flower is a tell tale sign, a foreshadowing of what is to come. That’s for the writer to decide.
However, I think the writer must stay consistent. If you’re using flowers in the story and use a lily to insinuate death or disaster, then you can’t just throw a carnation in later without thinking what that might mean.
Good stories have that layering that critical readers can spot and will enjoy. However, I think, too much can kill a story. As I said, if you’re using flowers as symbols stick with that. If you add flowers, the alignment of the stars, the colors of the curtains, and grandma’s foretelling – that might be too much. It’s like hitting the reader over the head with the symbolism and it’ll detract from the storytelling.