relating to 100 years : marking or beginning a century, with the example "the centurial years 1600 and 1700". But there is a word that is widely used to indicate the range of years or centuries covered by an article or book: history.
As you note, "percent" means "for every hundred," so there is nothing at all wrong with percent values greater than 100 when discussing proportions, e.g. profits increased by 120%. Like fractions, however, percent values are longer to express than multiples, so for values much greater than 100 you may hear them less frequently:
The flow rate increases 100-fold (one hundred-fold) Would be a more idiomatic way of saying this, however, the questioner asks specifically about the original phrasing. The above Ngram search would suggest that a one hundred has always been less frequently used in written language and as such should probably be avoided. Your other suggestion of by one hundred times is definitely better than a ...
37 Wikipedia lists large scale numbers here. As only the 10 x with x being a multiple of 3 get their own names, you read 100,000,000,000,000,000,000 as 100 * 10 18, so this is 100 quintillion in American and British English and 100 trillion in most (non-English speaking) other places.
"100%" is equivalent to "all". There is no rounding with "all"; either you get all of something or you don't. If a product advertised itself as "kills all bacteria" and then you found that there were 3 bacteria that it didn't kill, it doesn't matter whether that's 3 out of 10 or 3 out of 28 million; it's not all of them. Even in ordinary conversation, if your child says "I picked up all the ...