The potion does change the voice, as can be seen in the second book when the Polyjuice Potion is first taken.
Then he [Harry] realized that his glasses were
clouding his eyes because Goyle obviously didn't need them - he took
them off and called, "Are you two okay?" Goyle's low rasp of a voice
issued from his mouth.
"Yeah," came the deep grunt of Crabbe from his right.
(Harry Potter and the Chamber of Secrets, Chapter 12)
Then there's other evidence, such as that fake Moody in the fourth book could fool the people who knew the real Moody well, or other cases such as the Mafalda or Lestrange transformations from the last book.
The potion does change the voice, but not the person's natural speech patterns. In the case of an accent, there may be sounds it's difficult for the person to say, and also sounds that the person simply pronounces in a particular way, although also able to do otherwise.
In the passage you quote, it's likely that Fleur's natural inclination is not to pronounce the initial h-sound in "hideous", because of how her French accent works (we know from her other dialogue that she always treats initial-h as silent), so she maintains that distinctive pronunciation despite having her voice modified.
Another case potentially supporting this is just a couple paragraphs after Fleur's quote:
“The pairs will be as follows: Mundungus will be traveling with me,
by broom –“
“Why’m I with you?” grunted the Harry nearest the back door.
The "why'm" is typical of Mundungus Fletcher. For instance, this is him in the Order of the Phoenix:
'Some'n say m'name?' Mundungus mumbled sleepily.
(There's much more of the same in that book)
This would indicate that masterful deception using the polyjuice potion has a training element as well, as the person must train themselves to use the accent and speech patterns of whomever they are impersonating.