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In the sentence:
Bob does not know who/whom the thief is.
Should it be who or whom? and why? I don't really understand it in cases like this. I was told to think about them being analogous to him/he but it doesn't work here.
As I already explained, the answer given https://english.stackexchange.com/a/83/73786 does not work. Let me try it: Bob does not know the thief is he. It clearly should be Bob does not know the thief is him. That would mean it should be whom. Contradiction, no?
I think I understand your confusion. When "who" is clearly an acting agent, it's hard to make a mistake. In the sentence "Bob does not know who stole it", you probably wouldn't think of saying "whom". On the other end of the spectrum, you might have a strong feeling when you are dealing with an object: "Bob does not know whom to rob." Of course, here most people say "who" in regular speech, but if you try to look at the structure, you might be able to see that this "whom" is receiving the action, and thus it cannot be "who".
The problem with being verbs, especially "to be", is that they can appear to occupy a gray area between the actor and the object. Strictly speaking, this is because being (fancy talk: predicative) clauses are their own class; but since English is so hazy about case, there are no obvious indicators. What you should know is that existing is taken to be acting, subjective, however you want to think of it, and requires the "he" or "who" form.
Here's a more difficult version of your sentence, one that has given even very good writers trouble for a long time:
Bob does not know who/whom she thinks the thief is.
Who is the subject complement of is. Subject complements are either adjectives (predicate adjective) or nouns (predicate nominative). Thus, it requires the subjective (nominative) case for the pronoun.
To elaborate: Subjects are nouns, pronouns, or things acting as nouns (don't worry about this last one) that are the actor of a sentence (this is a very simplified analysis as there is more nuance than that). Nouns don't usually have case (except the possessive/genitive [John's]); pronouns do however inflect (change for case). The cases of pronouns in English are: subjective (nominative), objective, possessive, and reflexive/intensive.
Illustrated:
He is subjective
Him is objective
His is possessive
Predicates are verbs doing the action in the (main clause of a) sentence or linking subjects with other elements (again, this is simplified, and not a complete treatment). The type of verb you used (is) is a linking verb—it joins subjects with subject complements).
Illustrated:
John rode a motorcycle.
Frank is dumb.
Subject complements are either nouns or adjectives connected to the subject by a linking verb, such as is. In the last example, dumb is a predicate adjective because it is linked to the subject by is. An example with a subject complement that is a noun is:
John is a master. She is Jill. This is he.
The last example is not common in speech (fallen out of its very restricted use [answering phone calls]) and is normally replaced with him.
Now onto who/whom, who is subjective, and whom is objective. Any easy way to picture it is who represents he/they/she/it/I/you/we and whom represents him/them/her/it/me/you/us.
Your example stripped from the sentence and made into its own sentence with the exception of the place who substitutes:
The thief is X.
In everyday speech, people will say him, but grammatically, because the subject has a linking verb which takes a subject complement, it is he, or for your example (Bob does not know who/whom the thief is) who.
Bob does not know who the thief is.
Paraphrasing: He (not him!) is the thief, therefore who is correct.
There is no contradiction; in this case you should simply ignore the first clause (part) of the sentence (i. e. "Bob does not know"), we are not interested in it.
