Is it permissible to deal with online affiliate marketing companies that may display products which are not Islamically permissible, and consequently, to receive a percentage of their price?

There is no objection to participating in this work and taking commission for it. What you mentioned, that the customer might buy some forbidden goods, does not necessitate prohibiting this work entirely, as long as you do not know the customer's intent, and as long as the majority of the store's merchandise is permissible.