Yes, they will be full VS flight deck crews - initially, at least - and part-VS cabin crews, while locally-based crews are being trained. As I understand it, the A340s (don't know how many, but the first - G-VBUS - came out of the shed last week) will remain British registered for now, so the commanders will presumably be VS crew until that situation changes.
Virgin Nigeria isn't really my field of expertise (such as it is!), so I can only pass on hearsay stuff about it, which means don't take anything I say as gospel!