Here goes the longest description I've written on a submission thus far
Like many people, there are things I don't like about The Nine Realms
But Thunder's design isn't actually one of them

(some spoilers)
I'm NOT a biologist, but it's not entirely implausible to me that Night Fury characteristics carried on 1000 years after the third movie, presuming that there's nothing selecting them out of the gene pool
Seeing as at least two of Toothless' offspring (Night Fury + Light Fury) seem to have black as their base color (then with white markings added), it looks like black might be a more dominant/equally dominant trait
That'll then pass on to some of their (Night Light + Light Fury) offspring, then some of their offspring, and so on
No matter how many Light Fury enter the family, whatever genes code for that black color isn't just going to be wiped away. Maybe if those traits interacted somehow and Night Lights came in gray, but it doesn't look like they do that
Theoretically(?) Thunder's appearance in the show is totally possible without inbreeding
And the way I think about it, if any new genes were simply wiped out as carriers paired with non-carriers, evolution would be moot

Why the redesign?
I actually had Thunder's rider, Tom, in mind for this
All the (human) characters in Season 1 really liked to mention that time he climbed into a polar bear zoo enclosure when he was, like, five or something
Which is a funny detail to fixate on, considering it didn't really supplement the plot?
But what if Thunder actually was a polar bear-like creature, y'know? What if that one character detail tied into the story at least a liiittle bit, and Tom and Thunder's bonding wasn't a rushed parody of Hiccup and Toothless'
For as much as they try to bring the movies back into relevance in the show, I think it might've been better if they tried to step away, instead