VTEC have 2 main depots, Bounds Green (London/Alexandra Palace) and Edinburgh (Craigentinny). BD maintains 91/MkIV sets whereas CT maintains HSTs - mostly for East Coast but also for CrossCountry and Grand Central (the odd powercar ends up there every now and then for major exams/overhauls).
Newcastle is used for storage and presentation of VTEC sets. It's owned by Northern but services Grand Central's trains also.
I don't think it is a major task to apply vinyls (hell, East Coast got them all branded pretty much in a couple of weeks from NXEC) but even with failures and unsuccessful planning to get to the right locations, it's not brilliant that, as aureolin said, such a brand-conscious company cannot complete this.
One fully-branded HST set is due in traffic in May so I imagine it'll have been taken from service for a wee while now.
RE: East Coast / Virgin Trains East Coast