The Latin for thousand (not thousandth) is mille, and this survives in words like millennium for a thousand years and millipede for an animal with "a thousand feet." Similarly for cent- as a prefix in words like century; it comes from the Latin for hundred, not hundredth.
Just as in English, thousand/thousandth and hundred/hundredth are related, so they are in Latin: mille/millesima, centum/centesima. The -esima suffix survives in English in infintesimal.
In the SI system, Latin prefixes are used for subdivisions of the basic unit, as in millimetre and centigramme. The SI multiplicative prefixes are based on Greek: thousand is from χίλια; hundred in Greek is εκατό.
While it's reasonable to invent a system of measurements and use prefixes based in this way, evolved language doesn't work like that. Because language evolves, we don't generally end up with words where a prefix is Greek and the base word is Latin, like kilennium.
We can invent words how we like of course; one example is the SI millimetre, where the prefix is Latin and the base word Greek. Another (the other way round) is television, of which CP Scott, then Editor of the Manchester Guardian, remarked "The word is half Greek and half Latin. No good will come of it."