In order to have the bots run you must do the following: 
The Q3A CD must be in the cd drive. You can play multiplayer at a machine other than your dedicated server without having the CD in the drive.
You only need the cd for single player (or running bots on a server). 

Your batch file command line must have: +set bot_enable 1

Add the following commands to your server.cfg file: 

seta bot_minplayers 3   <--- how many people to join server before last bot leaves

seta g_spskill 2   <-- the skill of all bots. This is optional, otherwise it's random per bot

seta bot_nochat 1    <-- SHUT THE MOTHERS UP!!! :-)

After the map rotation cycle you should put the following: 

addbot slash 
addbot mynx

OR 

addbot slash 3   <-- if you want to specify skill level 

addbot mynx 2 90  <-- Give the bot a handicap health of for example 90 

However, after the first map change, the bots will be random unless you do the following: 

You can also specify bots per map like this: 

set d1 "set g_spskill 3; addbot sarge; addbot angel; map q3dm2; set nextmap vstr d2"

(if this i not correct please email me)
 

Note: if you do not set bot_minplayers then the bots will always be on the server!