the plug-ins you mentioned are all part of one VST3 bundle. It is located in the VST3 folder of the Nuendo program folder and is called “Nuendo Plug-in Set.vst3”.
Could you please check in Nuendo under Devices -> Plug-In Information for e.g. the Amp Simulator whether under “File” it indeed says “Nuendo Plug-in Set.vst3” and the “Path” is your installation path.
Are there any questions marks for the Amp Simulator in this line (indicating that the plug-in can’t be found)?
As these plug-ins are in a sub-folder of each Nuendo installation, 32 bit and 64 bit, installing Cubase won’t influence them. Are you using the VST2 or the VST3 version of other plug-ins that do work?
One thing you can try right away is the usual trashing the preferences. This way we will also force Nuendo to scan the plug-ins again.
You can also check under C:\Program Files\Steinberg\Nuendo 5.5\VST3 whether the Nuendo Plug-in Set.vst3 is available. Size should be roughly 11 MB and date should be 09/23/11 if you are on Nuendo 5.5.2.
If this is not helping feel free to get back in touch with me, either here, via PM or email.