there is not a univoque way because it not exist a unique version of the agent.
The Agent is made of different files (components) and some patches may modify some individual files only.
The only thing that I can think about is to look at the version of LDISCN32.EXE that is an executables that's common to all the agent configurations.
From DOS there is not a real direct way to have a look to the version of it (as far as I know): one way is to use FILEVER.EXE (part of the resource kit) or write a small VBS script that instantiates the FileSystemObject and retrives the version info of the file.
I uses to change the name of the agent each time I modified its configuration, or when I updates Landesk with a patch and rebuilt all agents.
Examples : 02 xxx Standard Windows Wks Agent V9.SP2-004.
03 xxx Standard Windows Wks Agent (+ARP Discovery) V9.SP2-004.
I have an agent configuration Number : 02 which identify the agent targets and its use. It never change.
Then The agent Name : Standard Windows Wks Agent.
Then the landesk Version and Service Pack : it could change depending of the service pack level...
Then the release version : -004 It change each time a change is done in the configuration (not very often) or when i patches Landesk with an MCP patch or others... (More often).
Then I can get them in queries and in inventory.
I hopes it will help you.