Yes. Many email marketing services treat affiliate links differently. Mailchimp, MailerLite, and Constant Contact don’t allow affiliate marketing. But you can still include affiliate links in your emails.
The difference is about purpose. If your main focus is making money from affiliate links, then that counts as affiliate marketing. You have to find an email marketing platform that is happy with you building campaigns around third-party promotions. The best affiliate-marketing-friendly email software include GetResponse, Moosend, SendX, and EmailOctopus.