Is money earned from working in customs clearance that involves paying bribes to customs officials to pass larger quantities of goods than what is registered in invoices—based on the merchant's request to pay lower fees—considered suspicious money?

What you have mentioned is circumvention and a forbidden bribe. Your taking a fee for clearing (goods/transactions) is permissible. However, what was taken in exchange for paying a bribe is forbidden, and you must dispose of it by spending it on the general welfare of Muslims and for the poor and needy. It is not permissible for you to benefit from it unless you are poor and in need of it. If you dispose of the ill-gotten money, along with repentance and a firm resolve not to return to it, then you have fulfilled what is required by Islamic law.