Learn Dutch: We wachten ermee zolang de goederen ontbreken. - We wait with it as long as the goods are missing.

Because zolang (as long as) is a subordinating conjunction. In Dutch, words like this introduce a subclause, which means the verb (ontbreken) gets pushed to the very end of that clause.

Where does the word ermee come from, and why don't we say met het?

Ermee is a pronominal adverb meaning "with it". In Dutch, you cannot combine a preposition like met (with) with the pronoun het (it). Instead, het turns into er and attaches to the preposition, which often changes form slightly (in this case, met becomes mee), giving you ermee.

I usually translate "missing" as missen. Why use ontbreken here?

While missen can mean missing a train or missing a person emotionally, ontbreken is specifically used when something is lacking, absent, or not present when it should be. Since the goods are physically absent, ontbreken is the natural choice.

The English translation often implies the future ("we will wait"), but the Dutch sentence uses the present tense (we wachten). Is that normal?

Yes, this is very common in Dutch. You can often use the simple present tense to talk about future plans or actions, especially when the context (like waiting for missing goods) makes it clear that it applies to the future.