The estimates are only as good as the available data. Flood designations are updated as more data are collected or when the conditions change in a river basin. In Washington, more than one 100-year flood has happened on a few rivers in just the past several years. The truth is that an uncommonly big flood can happen any year. The actual number of years between floods of any given size varies a lot.
Big floods happen irregularly because the climate naturally varies over many years.
We sometimes get big floods in successive or nearly successive years with several very wet years in a row. Scientists use statistics and observe how frequently different sizes of floods occurred, and the average number of years between them, to determine the probability that a flood of any given size will be equalled or exceeded during any year. As more data are collected, or when a river basin is altered in a way that affects the flow of water in the river, scientists re-evaluate the frequency of flooding. Dams and urban development are examples of some man-made changes in a basin that affect floods. These post-flood surveys are used to estimate maximum flows at sites that could not be reached during the floods and also to map the areas covered by the floods.