The second and third meanings are recent - 19th and early 20th centuries, respectively. The "plant" sense goes back to Old English, and is common in Shakespeare, as in the line "Lilies that fester smell far worse than weeds"
Complications arise with another "weed", which derives from a different source in Old English, meaning "garment". This developed a plural in the 14th century, a usage still heard today in "widow's weeds", and it is common in Shakespeare. There isn't a problem understanding it when the context makes it clear that the weeds are being worn: "Let me see thee in thy woman's weeds," says Orsino (Twelfth Night, V.i.270).
But when the context isn't explicit, it can mislead, as when Palamon sees "Scars and bare weeds" in Thebes (The Two Noble Kinsmen, I.ii.15). There is a nice pun on the two senses of clothing and plant when Marina says to herself, "I will rob Tellus of her weed" (Pericles, IV.i.13). Tellus is the Roman goddess of the earth. Her clothing is her flowers.