I have a kludge, but it only applies to Apple School Manager:
In addition to the locations with VPP tokens I have associated with Meraki, I created a "trash bin" location in Apple School Manager. The trash bin location token isn't sync'd with anything, so whenever I want to get rid of an app from the MDM, I move the licenses to the "trash bin" and then they don't show up in Meraki anymore - even on the VPP page.
If you're not using Apple School Manager, probably the best you can do is delete the apps from the App page of Meraki, but if the VPP licenses still exist, they'll show up on the VPP page. If you want the apps gone for good... you could try calling Apple and have them remove the licenses from your account? Don't know if they'll do it though.