When we sent out graduation announcements for our children, it was to share our joy at the accomplishment. Some people sent gifts, & my children sent thank you cards. Some people sent cards (no gift), & our children were glad that these people wished them well, but they sent no thank you cards.
When DH & I were married, some people were sent invitations to the wedding, others received wedding announcements. Some of both groups sent gifts, & some did not. Where gifts were sent, a thank you card was also sent.
I don't think you, or your son, need to send anything. The card was a way to share your son's accomplishment, & the cousin sent a card to congratulate. Would you send a thank you card to someone who sent you a birthday card? I don't.
I don't think it was a dig at you, but I personally believe that even if you knew it was, you should refuse to acknowledge the same. Altho decidedly not scriptural, I learned a long time ago that taking offense when offense WAS intended simply gives the one trying to offend you a certain amount of satisfaction. Choose to refuse delivery of the offense.
Just my thoughts