This is a very interesting observation. I do not know the answer for sure, so allow me to make some detours in order to approximate an answer. The starting point is your sentences:
- Willst du es auch?
- Willst du auch etwas?
I first want to examine the different positioning of «auch». In order to do so, I will make these sentences more normal by changing three elements:
- I will convert them into normal declarative sentences, since the phenomenon occurs there as well (cf. «du willst es auch» and «du willst auch etwas»).
- I will replace the short words «es» and «etwas» by a longer noun phrase, e.g. «den Kuchen» ‘the cake’.
- I will replace the modal verb by a proper verb (e.g. «essen» ‘eat’).
Like this, the sentences are changed, but the difference in the placement of «auch» is still preserved:
- Du isst den Kuchen auch.
- Du isst auch den Kuchen.
In (4), the «auch» is an attribute to «den Kuchen» as can be proven by the fronting test (auch den Kuchen willst du), whereas in (3), it is an adverbial constituent on its own right. The meaning of the attributive «auch» in (3) is restricted to «den Kuchen». The meaning of the adverbial «auch» in (4) applies to the entire sentence. This can be nicely illustrated when we further expand the «auch» into «nicht nur … sondern auch»:
- Du hast den Kuchen nicht nur, sondern du isst ihn auch.
- Du isst nicht nur das Brot, sondern du isst auch den Kuchen.
Now turning back to (1), the most striking observation is that it the word «es» is very unlikely to take the «auch» attribute as in (4), so the following sentence is highly unusual:
- Willst du auch es?
I think the reason is that the pronoun «es» cannot usually be stressed. Its usual pronunciation is with a mere schwa. The attributive «auch», however, stresses the word it is attributed to.
Turning back to (2), it is again striking that the word «etwas» is very prone to take the attributive «auch», so the following sentence is highly unusual:
- Willst du etwas auch?
This is more difficult to explain. I guess the reason has to do with the semantics of «etwas». Its meaning is indefinite. The way information is typically structured (cf. information structure etc.), it is the indefinite element in a sentence that is focused, because it is the new element that has not yet been talked about. This can be nicely illustrated by the use of the indefinite and definite article in languages such as English or German: when something is introduced, it takes the indefinite article (e.g. “once upon a time, there was a cake”). Subsequently, it takes the definite article (e.g. “… and the cake was delicious”). The attributive «auch» is a strong focusing particle. Consequently, if a sentence has an indefinite word, we expect any «auch» to be an attribute of that word. Note also what happens when I change the definite phrase «den Kuchen» in (5) and (6) into an indefinite «einen Kuchen»:
- Du hast einen Kuchen nicht nur, sondern du isst ihn auch.
- Du isst nicht nur ein Brot, sondern du isst auch einen Kuchen.
While (10) is perfectly acceptable, (9) seems puzzling (what cake are you talking about?) and more unusual than (5).