As split mentioned - there is no issue having both the 32-bit and 64-bit side by side. The trick is setting up the VST locations. I typically set up 3 locations. 64-bit only (Cubase 64 sees this, Cubase 32 does not), 32-bit only (Cubase 32 sees this, Cubase 64 does not) and one for both versions (both Cubase 32 and 64 see this).
So 64-bit dlls go in the 64-bit VST folder.
32-bit dlls that do not have a 64-bit equivalent go in the “both” directory, otherwise they go in the 32-only folder.
If a 32-bit VST that does not have a 64-bit equivalent that does not work in Cubase 64, and it needs to be JBridged, then the dll goes in the 32-bit only folder and the JBridged version goes in the 64-bit folder (which references the dll in the 32-bit only folder).
This basic set-up has worked very well for me and allows me to open a project in either Cubase-32 or Cubase-64.