Vortex cannot check for mod updates for Skyrim VR since it is looking for Skyrim VR on Nexus instead of Skyrim Special Edition on Nexus. All mods for Skyrim VR are under Skyrim Special Edition.
Additionally, you cannot endorse a mod using Vortex for mods installed in Skyrim VR for the same reason.
Either Nexus needs to add Skyrim VR as separate from Skyrim Special Edition or get Vortex to patch their code.
If Nexus does add Skyrim VR as a separate game, then it would be nice to include any Skyrim Special Edition mods that have been verified to work under Skyrim VR.