I am curious to see what the answer is to this thread as well. We only have half of our computers discovered.
I can't give you specifics on WHD, but for WMI yes there are a few dependencies that will need to be met on your systems.
First lets talk about the Packet traffic.
WMI initiates communications on TCP port 135. Once the session is set up the queries/request from WMI are processed on the Dynamic High End port range that can be anywhere from 1024 - 65535. If you are traversing a Firewall then look into setting up the DCE/RPC protocol on the Firewall. This will allow you to only need TCP port 135 open, and once the session is established the firewall will do a packet inspection and dynamically open up the High End ports that WMI is requesting for that transaction and then close it back down once completed. Also, make sure you don't have the Local (PC/Server) firewall on. If so then make sure you configure the rules to allow WMI traffic.
Second would be Account access.
WMI almost requires a full blown Admin to the local box or on the Domain to properly log in and be able to get in to the proper NameSpace or pass/run a WMI query. You can create an account that isn't a full admin and restrict the account through Policy control, but this can get cumbersome an have you trying to sift through MicroSoft Tech Net like crazy.
Last would be dependencies.
WMI requires RPC to be available as it's a direct dependency of the WMI Service. Depending on what information you are trying to pull as well Remote Registry will also need to be up and running and not in a hung state which can happen from time to time.
Hopefully this answers your questions about WMI and access to the computers you are trying to hit. If all of this is up and working then you have an issue with the local WMI agent and may need to try and re-install it, or install a 3rd party WMI agent and remove the Microsoft one.
I'm trying to discover our Virtual Machines and I am only able to discover 2 of them. After making sure the steps above are done, why would this be happening?
If these are XP machines support at WHD told me this was a bug and would be fixed in the next release. I'm having the same issue, its only discovering my servers.