The interesting, perhaps even innovative, thing about Danny's secret identity is that he doesn't have one to protect his loved ones, but to protect himself.
The whole point of Danny Fenton and Danny Phantom being "separate" people is so Danny doesn't risk being ostracized by his peers and dissected by his parents (all valid reasons), which contrasts greatly with how the Secret Identity trope is usually used.
Normally, a hero would have an alter ego to protect the people he knows and cares about from becoming targets.
In Danny's case, his secret identity doesn't do him any favours when it comes to that. It doesn't protect anyone but himself, he does the saving and protecting.
Literally every single enemy/adversary he has except Valerie knows who he is. They know him as Danny Phantom and they know him as Danny Fenton.
Hell, his whole dynamic with Vlad is built around the two of them knowing each other's secret identities!
Moreover, his enemies have exploited his secret identity and his weaknesses against him many times already, targeting people close to him in the process:
Ember used his closeness to Sam to cast a spell on him and make him care about nothing but her.
Technus used his feelings for Valerie to distract him while he was busy decoding.
Spectra humiliated him at Casper High to feed off of his misery.
Kitty possessed Paulina to make Johnny jealous, and she originally was after Sam...
Do I need to go on?
Danny's secret identity does nothing to protect the people he cares about because every single person it should protect them from (again, sans Valerie) knows who he is. What his secret identity does for him is allow him to live a, relatively, normal life, saving him from having to live his greatest fears. Fears which are all part of his civilian identity, not his superhero persona.
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