What is the ruling on working in a factory whose owner deceives customers by having part of the order manufactured in another factory, and evades customs duties, knowing that I do not assist him in the evasion, and am I sinful for not reporting these practices?

If your work in the company is not related to deception or assisting in sin, then there is no harm in it. You must advise your employer regarding his violation of the contract terms with customers, and threaten to inform customers or the competent authorities if he does not stop. If he does not desist, and you are able to inform customers or the competent authorities without harm to yourself, then you are obliged to do so, based on the hadith "Religion is sincerity (or advice)." As for evading unlawful taxes, it is permissible, but if they are lawful, then it is not permissible to circumvent them.