The MQLIST command gets the MQ subsystems from the SubSystem Vector Table (SSVT).
In order to do not see an old MQ Subsystem in the list returned by MQLIST the MQ subsystem should not be in the SSVT.
If you want to delete the old MQ Subsystem you could try to delete it from SSVT using the SUBSYS command of Sysview.
The Sysview command SUBSYS can be used to display information about subsystems and there is a DELETE sub-command to delete subsystems.
Please note that the deleted entries will not show up till the next IPL. Once the system is IPL’d the entry will be back.
If you want to delete it permanently, if it is truly no longer used, the proper and permanent place to delete it from is the MVS parmlib member IEFSSNxx. Since here is where the MVS subsystems are defined in.