No, it wasn't. While this was the 100th episode, it was really his 99th case. The confusion comes in because the first case,
Mr. Monk and the Candidate (2002), was a two hour pilot movie and subsequently syndicated as a two part episode.
The next one,(
Mr. Monk Gets Hypnotized (2008) ), is his 100th case.
What more, there is some confusion due to the end of another episode (
Mr. Monk and the Big Game (2006)), where it is said that Monk had solved 104 cases. This number presumably includes cases he had solved while a member of the Police force, and those wouldn't count here, as this episode commemorates the cases solved as a Private Detective.