Learn French: La pollution est plus nuisible que je ne croyais. - Pollution is more harmful than I believed.

This is the ne explétif. It is often added to the second part of a sentence after a comparison of inequality (like plus... que or moins... que) when the main clause is affirmative. It doesn't mean "not"; it just emphasizes the gap between reality and your past belief.

Is the ne explétif mandatory here, or could I just say que je croyais?

It is optional. You can absolutely say que je croyais, and in everyday spoken French, that is actually much more common. Adding the ne explétif makes the sentence sound more formal or literary.

If the main clause were negative, would I still use ne here?

No. The ne explétif is only used when the main clause is affirmative. If you were to say La pollution n'est pas plus nuisible que je croyais (Pollution is not more harmful than I thought), you must drop the extra ne.

Why use the imperfect tense croyais instead of the passé composé j'ai cru?

You use the imperfect here because it describes an ongoing state of mind or an opinion you held over an unspecified period of time in the past. The passé composé would imply a sudden realization or a specific moment of belief, which doesn't fit the context of having a prior general assumption.

I've also learned the word for harmful. Could I use it instead of ?