Yes. You can always be charged but that doesn't mean you can be convicted unless they can prove the case. You should hire local CA counsel ASAP. If you can not afford counsel ask the court for a free public defender (PD). If the court finds that you financially qualify they will appoint a free PD. No one can guarantee you an outcome but there are obvious issues that are apparent regarding both the stop and the search. Your lawyer will recognize and address those with you during your consultation. Good Luck. Hope this helps?
You can be charged with paraphernalia for the crack/meth pipe, but remember that it is on the government to prove that you knew about it. I'm guessing that you were issued a citation, and that citation will have instructions for how to appear in court. The first date is just an arraignment where you will enter your plea to the charges. I would definitely recommend at least consulting with some attorneys. If nothing else, you'll have a better understanding of the situation at no cost to you. Hiring an attorney, on the other hand, while pricy, puts someone who is on your side and devoted to a good outcome for YOU. There are no guarantees, but having an attorney on your side is the best thing you can do for yourself at this time.
Bottom line - you need a lawyer - either one you select and hire or the public defender if you financially qualify and they're appointed by the judge.
There may be legal issues with the search - you don't give enough details that would justify WHY they searched your car. Don't post them on line - this is something to discuss with your lawyer.
To answer the question more directly that you asked - can they charge you? Yes. Can they convict you? That depends on whether they can prove beyond a reasonable doubt that you knowingly possessed it.
The above answer is for general information only and is based on the information you posted. Every case is fact dependent, so to get a thorough analysis of your situation, you will need to consult face to face with an attorney licensed to practice in the jurisdiction where the incident took place. Do not conclusively rely on any information posted online when deciding what to do about your case.