When referring to 1800 as just a number, it's fine to say either "eighteen hundred" or "one thousand eight hundred". When referring to the year, we nearly always say "eighteen hundred". In terms of other number, like 9900, yes, you can say "ninety nine hundred"; however, the bigger the number is, the less likely we will that way of expressing it - we would more likely say "nine thousand nine hundred".

While you can say eighteen hundred, one thousand eight hundred is the more correct phrase. If you do say xx-hundred, then you would only say it for numbers that end 1-9, for example "fifty four hundred" would sound acceptable, but "fifty hundred" would sound strange.

You can say either, it is less formal to use the "eighteen hundred" format but sometimes it is used because it's less syllables or has a more pleasing sound to it. Saying a year is in an odd format too: 1066 is "ten sixty-six" and 1945 is "nineteen forty-five.