You should have joined the codex long ago man.
Well I had lurked here for some time; and it looked such a friendly, warm, and all-accepting kind of place that it took a Mechajammer-induced level of trauma for me to come seek a measure of comfort amidst your ranks.
Here is my theory:
Hermione entered Hogwarts and as a result she got cover from her "government" (wizards) which has ties to real government (Muggles). This ought to take care of most of the official paperwork. While she was on the run I doubt that the evil mages were considerate enough to inform the Muggle government what's going on. If anything they most likely wanted to catch her themselves. The situation with the Ministry of Magic prosecuting a wife of a guy when Harry & Co infiltrate the Ministry of Magic is good enough example.
I'm thinking along those lines too.
We know that the Ministry Of Magic has a modicum of association to the government in Number 10, and possibly a bit of influence also. So I don't think it's too far-fetched to conceive such a notion would see Hermione modifying her parents' memories before asking for some help at a later date, perhaps on the part of Arthur Weasley, to cover what tracks she had not been able to touch. Extraordinary times, extraordinary measures and all that.
Withal, for Hermione, expunging the Muggle-kept records of herself is not even an imperative. The idea they have to be cleaned is predicated on the unlikelihood of evil wizards' rifling through them in order to find Hermione's parents; but we know such wizards are outright disdainful of all things Muggle, and I'd be really surprised to discover any pure-blooded, cousin-humping, lineage-touting supremacist who would even know where to begin searching after such records. And if a computer is involved, well, that's pretty much game over.
She got most of her expenses either covered earlier (when she had support of her parents) or by the school itself (I can't remember if school sends uniforms to the students via owl-mail or they get them on-site). I could be mistaken, but I think you had to pay in gold/cash back then, so there shouldn't be that many bank records and if there were, who really suddenly wakes up to check bills from years back?
They have to buy their wizard robes themselves before they even step foot aboard the Express.
And yes, absolutely, there wouldn't be many financial traces of Hermione's existance after her entry into Hogwarts. The specifics of converting pounds or whatever kind of Muggle money into Knuts, Sickles, and Galleons are never explained, but I always thought Muggle parents would simply withdraw some cash from their bank, before walking into Gringotts where the goblins would exchange it.
Now this explanation of hers has go to be one the worst, most maladroit pirouette I've ever seen attempted to get oneself out of trouble; because anent the two thugs, there was precisely zero need to wipe their memory and a 'simple' modification would have proved equally useful, possibly even more.
...assuming that modification is easier than wiping.
Oh on the whole, when altering the most minute details of memories years or decades in the making, it has to be harder! But in that specific instance, with Hermione having previous memory-altering experience to boot, I can't imagine it would have been harder for her to point at the pair of thuggish wizards she, Ron, and Harry had just beaten into unconsciousness, and make the pair believe they had encountered not Potter & Friends, but rather some random wizard who had uttered the taboo-stricken monicker of Voldemort.
Man, speaking about all that, I really do wonder what her editor thought. I noticed he had let slip some very basic errors like confounding jealousy with envy, poisonous with venomous, and things of a like ilk, so perhaps he wasn't bothered about the little details and was focused solely on the big-picture stuff?
Oh well. We'll see if Rowling decides to retcon yet more things in Hogwarts Legacy. Perhaps it'll be revealed Godric Gryffindor and Salazar Slytherin were an item, and the whole anguinous imagery will take a different meaning?