A century goes from 1 to 100, extremes implied, so "Il XVI secolo" is from 1501 to 1600.
The year 1600 is still XVI century.
It isn't so named only in Italian, but in other European languages too but, il Cinquecento, il Seicento and so on, must be considered in the context (historical, scientific, philosophic, artistic etc. one) because usually those limits aren't so strictly defined.
It isn't "sedici" because ordinal numbers are used (and not only in Italian). Have you ever read "In the first century A.D/B.C."/Nel primo secolo..." or similar sentences ?
V = quinto secolo
VI = sesto secolo
etc.