If I’m being accused of stealing pills from a house I was doing work on can I get charged?

Any person can be charged by a prosecutor who thinks they can prove them guilty beyond a reasonable doubt of committing a crime. Whether you can be convicted is a whole other question.

You can be charged, but that doesn't mean you will be convicted. They still have to prove your guilt beyond a reasonable doubt. Is there any other proof besides what you stated? Was there other people that had access perhaps? This is a typical larceny in a building case that can be tough for prosecutors to prove because often they are based upon the victim's word alone. Do not speak to the police or agree to take a polygraph. Be proactive and consult with an experienced criminal defense lawyer now. Do not wait until you are charged. A good lawyer may even be able to dissuade the police or the prosecutor from filing charges.

Yes. Had you under suspicion no doubt.

If they were paranoid to the extent of counting pills, then why do they ever have anyone over? They have to prove that you took them.

I believe that you have asked this question before, and the answer remains a yes, you can be charged based upon such information.