There are 3,141 counties and county equivalents in the 50 States and the District of Columbia. They are categorized as follows:
Proposals to change the name of a natural feature may be submitted to the U.S. Board on Geographic Names as described below. However, there must be a compelling reason.
Yes, GNIS actively seeks names of features that no longer exist. There are more than 100,000 such entries in the database now. To search for them, type the word "(historical)" (along with other name words if desired) in the name field.
The USGS Geographic Names Project maintains an active and extensive program to add features not in the database, primarily through partnerships with Federal, State, and local agencies, and with other organizations having relevant data.
One might confuse the difference between degrees/minutes/seconds and Decimal Degrees. To convert from decimal degrees to degrees/minutes/seconds with 45.63248 as an example:
All coordinates in the database are in NAD 83. They were converted from NAD 27 in September 2005. 
Often, users of the data can misinterpret the content of certain fields. The field entitled "USGS 7.5' map" may be one of these fields.