The only reason the Clinton Co simulcast site would be in the RRDB is because someone heard it, verified it, and submitted it to the RRDB. If the site is not on-line then it should not be listed in the RRDB.
The reason why they have different frequencies and site numbers is because they were thought about and created at different times. Apparently after the single site (Site 5) was in place, somebody decided that didn't offer enough coverage for the county. The 'powers that be' decided they wanted to add 2 more tower sites to the county, while also incorporating the original site, to create a 3-sitev simulcast cell. When it's all said and done Site 5 will likely not exist anymore.