We sat under cover, angry and upset when the fireworks ceased.

The adverbial clause 'when the fireworks ceased' modifies the (verbless clause) adjectives 'angry and upset.'

However, the adverbial clause says when we were angry. In other words, the adverbial clause must be modifying the implied verb of the adjective phrase, correct?

Is this allowable? Should I refrain from using verbless clauses when the omitted words are the ones beng modified?

Angry and upset are simply adjectives.
Agreed; they are adjectives. But it is also a verbless clause: http://www.novalearn.com/grammar-glossary/verbless-clause.htm

And the adverbial clause can't answer when someone was angry without a verb being present.
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What do you mean,'answer'?
As you know, adverbs modify adjectives or other adverbs, answering a question, like when, where how.

When an adverb answers a question like when, it is modifying the verb:

I searched for my wallet, when I returned from my friend's place.

Underlined clause modifies the verb, answering when I searched.
You make it difficult by mispunctuating: no comma.

So...? The adverb is sentential; it does not modify the verb only; it modifies the main clause.
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'And the adverbial clause can't answer when someone was angry without a verb being present.'

- why? In many kinds of fiction (even classical works by reputable authors), it does.

The sentence combines two clauses:

We sat under cover. + We were/sat angry and upset when the fireworks finished.

The when-clause has a shade of reason, as if explaining why they were angry and upset; alternatively, it can be viewed as a time clause. In my view, it has scope over the entire verbless clause. Since the verb in the original presumed utterance is copular and carries almost no real content, it is omitted without any detriment to the when-clause, as it doesn't only refer to the verb.

Respectfully, Gleb Chebrikoff
OK, thank you to you both. I suppose the analysis of what exactly the adverbial clause modifies is subjective. When I wrote the sentence, I tried to make it read so that it modified only the omitted verb, for the purpose of the question.