Employment is at will in California, absent a collective bargaining agreement (union) or an individual employment contract. So, the employer is free to change the rules applicable to the workplace -- by adopting an employee handbook or manual -- at any time and for any reason. Employees who find the changes unacceptable are free to leave the position.
Management has the right to make an individualized decision in cases of employee misconduct. Here, management decided for some reason not to fire the manager accused of stealing. It is not required for management to disclose its reasons, and the failure to fire that employee does not give rights or protections to other employees who are suspected of stealing or lesser forms of misconduct.
Management directions for searching of employees are allowed if the search is not unreasonable. Inspections of bags, pockets, purses, etc. have been upheld as within management's discretion for combatting theft and breaches of security re proprietary information. A full-body search of each employee at the end of every shift would not be upheld -- it is too great an intrusion and out of balance with the managerial interest on which it is based.
Unless the employee handbook and/or management policies are applicable only to employees of a certain race, religion, gender, etc. (i.e., a prohibited basis for personnel decisions) management's rules do not constitute unlawful discrimination.
It is not clear from your question what kind of "searches" the employer intends to implement. A search of an area where an employee has a reasonable expectation of privacy such as a desk, office or locker secured by a personal lock is very likely unconstitutional under the California and U.S. Constitutions. Nor can the employer conduct a personal search of an employee's personal belongings without a showing that the search was both work-related and reasonable under the circumstances. If the employer is conducting these types of searches, I strongly advise you and your colleagues to immediately consult with an attorney.
The response given is not intended to create, nor does it create an ongoing duty to respond to questions. The response does not form an attorney-client relationship, nor is it intended to be anything other than the educated opinion of the author. It should not be relied upon as legal advice. The response given is based upon the limited facts provided by the person asking the question. To the extent additional or different facts exist, the response might possibly change. Attorney is licensed to practice law only in the State of California. Responses are based solely on California law unless stated otherwise.