Perhaps I am just missing something obvious, but is there a way to run a single report that will list the number of agents for each machine group?
It's not a report, but take a look at the Licenses tab on the [System > License Manager] page. The number of agents in each group are listed under the "Agents Used" column.
This SQL gives you a count instead of a list, but that is easy enough to change.
SELECT mg.groupName, COUNT(Machine_GroupID) FROM [ksubscribers].[dbo].[vMachine] m
INNER JOIN [ksubscribers].[dbo].[machGroup] mg ON (m.groupName = mg.reverseName)
GROUP BY mg.groupName