It could have a negative connotation. One could be a genuine wise man or essentially a snake oil salesman, so the word could be applied in both ways. It's like how we use "genius" as an insult; we're using the word in an ironic and sarcastic way.

Here is a collection of various uses throughout history:

https://www.oed.com/dictionary/wizard_n?tab=meaning_and_use

Yes. It's not too unusual for that sort of thing to happen. Feverfew and lungwort are plants named after their medicinal uses, and the tea plant and rubber tree are named for what they produce. Wheat means white, referring to the ground flour.

A lot of things might have had other names before a use was discovered, or they just might not have been named by anyone yet. I think most plants have probably had lots of different regional names within the same language. Flowers seem to collect a lot of names; I think they make us poetic because they tended to interact with human culture in many ways.