I could be wrong, and someone else can probably correct me or elaborate better, but I don't believe removing the queues from the package will cause the package to uninstall any queues already on a user's workstation. In other words, if you take a queue out of the package, that queue won't get installed when you run the package on a new workstation, but on a workstation that already had that package installed, it won't remove the already-installed queue.
Hope that helps!
The answer to your question may depend on a few things. For starters the registry keeps track of which packages are installed [HKLM\Software\Wow6432Node\Pharos\Installed Packages\Popup Printer], for each popup printer installed, there is an associated spool queue ID. As best I can tell, Pharos tracks the package and the spool queue ID in order to determine whether or not the printer should deleted and recreated with the updated name.
For example, say that you created a package - "Package A" - that contained "Popup Printer A" associated with "SpoolQueueA" on "PrintServerA". You then renamed the Queue > Workstation Display Name in Pharos Admin and created a new package - "Package B" - that contained "Popup Printer A Renamed" associated with "SpoolQueueA" on "PrintServerA". I would not expect the original "Popup Printer A" to be updated to "Popup Printer A Renamed" because the package ID is different. If instead, you had simply rebuilt and reinstalled the original package ("Package A") after changing the Queue > Workstation Display Name in Pharos Admin, I expect that it WOULD update if it behaves as my system does.
I may be wrong here in that the popup printer entries in the registry do have an associated Pharos spool queue ID, and that may perhaps result in it getting updated as long as the spool queue ID's matched (even if not part of the original package), but I did not go to that level of testing. I do know that if you install a package, update the workstation display name for the queue(s) you just installed, then you rebuild and reinstall the package, the popup printer names on the workstation will update as well. Someone at Pharos may be able to comment more conclusively without having to do any testing.
Removing a "Queue" from a Package will not cause it to be removed from the client machine when the UniUpdater next runs.
To Stevens comment: Because of the spool_q_id in the registry the existing print queue on the client will take on the updated "Workstation Display Name".
If you install "Package1" for Queue1 with a "Workstation Display Name" of Printer1 on a client the client now has a print queue on it called "Printer1". Now modify the "Workstation Display Name" for this Queue in the Pharos Administrator and change it to "Secure1" and create a new Package called "Package2" with the same Queue in it. Once I build and install this Package2 on the client machine the print queue on the client is now using the new "Workstation Display Name" of Secure1. Because it is the same queue the current queue on the client gets changed, no new queue is added to the client.
The Workstation Display Name was built into the Package so if I simply re-install the original Package1 back on the client it will change the print queue name on the client back to the original one of "Printer1".