I think it's a type he's attracted to. Just like Marilyn Manson always dates women who have pale skin, dark hair and dress feminine. To give you another example of someone with those same eyes that Nyk openly said he is attracted to: the drag queen Courtney Act.
I am also reminded of something I once read about the muralist Diego Rivera. In his murals, he would sometimes draw his wife Frida Kahlo but he would also include the women he was cheating on Frida Kahlo with.
There was this one mural where he drew Frida with normal, dark eyes, but his mistress in that mural had bright eyes, much like the transwomen Nyk is attracted to. Supposedly Diego drew his mistresses with bright eyes to let the viewer know which woman was his sexual favourite. I suspect that Nyk, like Diego Rivera, views bright blue eyes as an indication that someone is sexually "up for grabs".
Nyk has brown eyes from his Italian side, and he basically hates anything about himself that reminds him of being Italian. We have often speculated in this thread that the reason Nyk is so obsessed with Natsees and white supremacists is because he too has a racial bias when it comes to dating: he is attracted to women who look white Western-European or "elven", which he as someone with overt Italian genetics does not look like, but is using his transition to approximate as much as possible. Nyk originally was a dark-blonde, but when he trooned out he became a light-blonde. Bleeching his hair was part of approximating that aesthetic he likes in the women he's attracted to. Or, to give yet another example, why does Nyk hate his body hair? Because Italians with their dark Semitic body hair are more visibly hirsute than white Western-Europeans with their blonde body hair. When Nyk had FFS, the facial features that he wanted to change were his Italian features, especially his nose. It was essentially Facial Westernization Surgery, not Facial Feminization Surgery. So I would guess Nyk is attracted to bright blue eyes because he really is attracted to that "Aryan" aesthetic of "blue eyes, blonde hair, fine/elven facial features", but he hates himself for it because he's an SJW and he should be able to overcome his "racial bias" in dating.