What is it called? VS What is it spelled?

This is essentially true (call, spell).

The logic to justify this usage is simply that a concept is being made to correspond to an element of a set, the set of representations, which are words, and the concern is with which element does that or, said otherwise, with what element is suitable for representation; therefore "what" is the natural word that is being suggested. When dealing with spelling the concern is with the means of implementing a code (how to implement the graphic form properly) and thus the word that is being suggested is "how".

Notice that in the ngram above the form "How is it called?" although not found nowadays has been used in the past (18th century), for instance in this source. This is because the alternative of thinking of words as arrangements of sounds or letters is what instigated the choice of wh-word: "How is the arrangement of sounds (letters)"; as this way of thinking is rather indirect, not what is obviously more relevant, it's not been preferred. One might wonder, by the way, whether or not this latter manner of asking this question should not be due to a certain extent to the influence of French, a language in which "how" is the usual word for this question (the situation is reversed (ngram), comment=how, qu'est-ce que=what) .

How can always be replaced by "In what manner..." or "By what means...", "What must I do to..." It asks for the method by which the verb is done.

Thus we can say "How is it spelled?" because the meaning is "What is the method to spell this?" and (possibly idiomatically) the answer is the letters needed.*

"How is it called?" meaning "What is the name of this thing?" doesn't make sense: if you want to know the name of something, then "In what manner..." "What must I do to..." "What is the method for..." are inappropriate. As Greybeard comments, call in such a question means call forth, or summon. "What is the method to call it?" does make sense and "How is it called" is valid. You would get the answer "You speak its name."

So, if you want to know what its name is, the correct question is "What is it called?"




*An exceptionally obtuse answer would be "You write the correct letters in the right order," but even "How do I spell that?" (rather than "How is that spelled?") doesn't really warrant that answer. Using the verb spell asks for information about the spelling rather than how to write.

Here are some questions together with the answers you might get from a native English speaker

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Q: What is that animal called?

A: It is called a dog. English people call it a dog.

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Q: How is that animal called?

A: It is called by blowing a whistle. We call the animal to us by making a high-pitched sound.

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Q: How is that word spelled? The word you just said?

A: I said the word "family". It is spelled F-A-M-I-L-Y

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Q: What is that word spelled?

A: I'm sorry, I don't understand the question.

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Note

The verb "to call" has many meanings. You may be confusing these meanings although originally they came from the same root. Examples:

Wife: I call my husband John by shouting "John!" very loudly because he is slightly deaf. In this case "to call" means to request someone to answer you or to come to you.

Mother: I call my son John, "Jack" because he prefers that name. In this case to call means to address someone or to mention their name to a third party.

It may be helpful to look at all of the W's.

Why was a thing made out of what? Why versus what. As in the nature of things.

Who owns which animal? Which type of animal? Who versus which. As in, which spelling is correct according to whom?

Can't understand how unless know this or that. How versus this and that. As in, how to spell a word carefully upon some research.

When will you be where? When versus where.