Is "Who art" correct?

Solution 1:

Yes, "thou (...) who art" or "thee (...) who art" are correct.

I wasn't sure from the title whether you were asking about relative pronouns or interrogative pronouns, so I will discuss both in my post.

In the hymn that you quote, the relative pronoun "which" takes second-person singular agreement because its antecedent is the second-person singular pronoun "thee". This is a special thing that happened/happens in old-fashioned or formal English' related questions about this topic are What rules make “Remember me, who am your friend” grammatical? and "Me who is" or "me who am"?

In terms of interrogatives, "Who art..." would be possible in a sentence with "thou": "Who art thou?" In modern English, sentences of this type (e.g. "Who am I?") are best analyzed as having "who" as the (fronted) predicate rather than as the subject: a piece of evidence that "I" and not "who" is the subject of "Who am I?" is that we can't say *"Who am me", even though in predicate position "me" is usually possible (we can say “It was me,” regardless of whether it’s considered “incorrect” from a prescriptive point of view). In older varieties of English, I'm not sure whether there is any clear way of establishing which word is the subject in questions like this.

Solution 2:

The language is archaic (the hymn was written in 1861) on purpose.
Compare this to the Lord's Prayer. Matthew 6:9 reads in the King James version: "Our Father which art in heaven, Hallowed be thy name."

The construction "which art" was current in the 17th century, but uncommon yet understood in the 19th. The lyricist Reginald Heber meant to match the older style

The lines in question,

Cherubim and seraphim falling down before Thee,
Which wert and art, and ever more shalt be.

are based on Revelation 4:8:

And the four beasts had each of them six wings about him; and they were full of eyes within: and they rest not day and night, saying,
Holy, holy, holy, Lord God Almighty, which was, and is, and is to come.

(KJV)

So the verbs wert, art, shalt be, are correct in an archaic usage and are used here for their poetic value.

Hope this helps.