As Andrew has said in his comment, you don’t need brackets here. By using them you create an unnecessary difficulty, and you don’t really need to replace them with commas. San Diego and its surrounding areas is a plural subject, so it needs a plural verb.
What you also need is the verb in a different tense. The second clause in the sentence is, in functional grammar terms, a projected clause. That is, it is similar to indirect speech, in which present tenses normally become past tenses. All these considerations point to writing the sentence as:
I had no idea San Diego and its surrounding areas were that crowded.