If you look at a lot of the old pictures of rockers and their bikes you will notice half or more are stock bikes with a few things removed, stock seat, drag bars, etc. They were also riding fairly current bikes, they weren't restoring 40 year old motorcycles. Who knows who actually coined the term "cafe racer" but I am betting it started as a derogatory term referring to the kids being wanna be race bike riders.
Ive also spotted a few jap bikes hiding in a few old pictures of the rockers and their bikes. I'd imagine they mostly rode British because that's what they had, if a faster Jap bike could be had for the same price with the same parts availability they probably would have been more common.
I have friends with new bikes and old bikes and I consider some of the new ones, including a new Thruxton, to be cafe racers because they are true to the style and ridden with the same spirit.
I've also seen vintage bikes with clubmans, bum stop seats, open exhausts, and pods that I would not consider cafe racers because they were just slapped together and probably don't perform any better than they did stock.
Chrome wont get you home and clubman bars and pipe wrap don't make your bike any faster! I'd trade my old Honda for a new Triumph any day, they are nice bikes and if it was mine it would be a "cafe racer" because I'd rid it like it is.