I'm quite familiar with multiple IRT models; however, I can't seem to understand the Nominal Response Model. How is theta estimated? For example, if we have a science test with multiple-choice items ("Which one of the following is an animal?" A) chair, B) cat, C) owl, D) sunflower), how does the model "know" which answer reflects the greatest knowledge? Do I have to put the answers in "logical" order myself (as 0 - chair, 1 - sunflower, 2 - owl, 3 - cat), so the bigger the category, the "righter" the answer? Or do I have to add the key to the model?
No, you don't have to add the key. Adding a key to multiple-choice data like you describe would be equivalent to fitting the two-parameter logistic (2PL) model if "0" were to be assigned to all response options except for the correct response.
It's quite confusing because I've read everywhere that the answers can be unordered (that's why it's called nominal for sure). However, if I do not add the key or reorder the answers myself in a logical way, then I really can't understand how the ability/theta is estimated.
So, if I understand this part of your question correctly, you are asking how the IRT estimation algorithm "knows" which response option is indicative of the highest $\theta$ level. To understand how this is done, it is first important to realize that not all nominal data is appropriate for the Nominal Response Model (NRM; Bock, 1972; Thissen, Cai, & Bock, 2011). Revuelta, Maydeu-Olivares, & Ximénez (2020) make this clear by differentiating first choice data - a type of nominal data appropriate for the NRM, from other types of nominal data.
We need to distinguish between two kinds of nominal
data. Usually, when we think of nominal data we think of
purely unordered data such as country of residence (1 = US,
34 = Spain, etc.). In these cases, factor analysis is not
applicable. However, in some cases, we can conceive of
the existence of an underlying order among the response
alternatives, with the observed outcome being the result of
a decision-making process. For instance, if we ask “in what
country would you like to retire?”, we could use the same
numeric codes as before, but the obtained data would be
different; it would be first choice data. In first choice data,
we assume that the respondent orders the alternatives in her
mind but only provides her top choice to follow the instructions received (Bock, 1997; Maydeu-Olivares &
Böckenholt, 2005, 2009). First choice data is still nominal
data, as the response alternatives are unordered. However,
because of the assumed underlying order, one of the major
tasks in applications is to ‘uncover’ the ordering of the
alternatives presented.
Now, regarding how this is done, I suggest @Christian Hennig's answer as they address this very well. Though, in a few words, the NRM does not make any assumptions regarding the "correctness" of a response.
References
Darrell Bock, R. (1972). Estimating item parameters and latent ability when responses are scored in two or more nominal categories. Psychometrika, 37(1), 29-51.
Revuelta, J., Maydeu-Olivares, A., & Ximénez, C. (2020). Factor analysis for nominal (first choice) data. Structural Equation Modeling: A Multidisciplinary Journal, 27(5), 781-797.
Thissen, D., Cai, L., & Bock, R. D. (2011). The nominal categories item response model. In Handbook of polytomous item response theory models (pp. 43-75). Routledge.