With races like Doppleganger and Cyborg, that create bots on the map, I'm assume you would have to be playing on a regular cs map that comes with the game? because on custom maps, it does the whole scanning thing so the bots know where to go... If a player comes on the server with a custom map on and uses a race that uses bots, and spawns bots, will it cause the server to pause and start scanning for the bots where to go?

And if it does do this, and the person leaves, will it have to do it again if someone else uses a bot race?

no Hoofi is right.. this happened to me with the map fy_thewall
i changed race to Doppleganger and right away the server went into the scanning mod and no one could play untill it finished

If you are using BOT RACES you should have bots enabled..

If bots are already enabled it will already have a .nav file.