My question is if there's any "danger" of having an old viewlet
registration to a previous viewlet manager since we changed to the new
viewlet manager only on configure.zcml and didn't use a hidden directive
in a viewlets.xml.
Since yours was a custom viewlet, just chaging the configuze.zcml moves it to the new manager. The problem of having it registered to multiple managers happens with viewlet overrides, since the override is pointing to a different manager than the original.
You can double check by exporting the viewlets.xml from portal_setup to see if the viewlet is only listed in the new manager.