The thing that indicates whether a vst appears on the RegionFX view or not is it's "isARA" flag in the registry.
All the plugins Cakewalk is aware of are stored here:
Computer\HKEY_CURRENT_USER\Software\Cakewalk Music Software\Cakewalk\Cakewalk VST X64\Inventory For Sonar Platinum, it's here:
Computer\HKEY_CURRENT_USER\Software\Cakewalk Music Software\SONAR Producer\Cakewalk VST X64\Inventory Since you've uninstalled Autotune, you can probably delete the keys associated with it, but setting it's isARA to 0 rather than 1 will remove it from the RegionFX menu.
Note: there's probably more than one entry for Autotune, and only one of them will have the isARA set to 1.
As a side note, I've also found that Antares plugins don't behave well with Cakewalk. The fix for me was to disable the VST3 version (either by renaming the plugin on the filesystem to .vst3.old and rescanning, or deleting the registry keys for the vst3 version) and just work with the VST2 version.