Cost per click was more common in the early days of affiliate marketing but has diminished in use over time due to click fraud issues very similar to the click fraud issues modern search engines are facing today. Contextual advertising programs are not considered in the statistic pertaining to the diminished use of cost per click, as it is uncertain if contextual advertising can be considered affiliate marketing.
Always disclose your affiliate relationship. Most visitors will probably understand that graphic ads will lead to your getting paid, but if you write a review or use an in-text link as a recommendation, you want your readers to know that may lead to compensation as well. This ensures you retain transparency and trust with your readers, but also, it's required by the FTC's endorsement rules.