To answer the OP question then no, totally merged traffic 1000ft apart will not be affected by wake. There are instances however where traffic following a few miles behind 1000ft below have encountered wake (and sometimes offset depending on wind direction and strength). The main culprits giving off wake in this manner are the A380, MD11 and B757 (I think the -300 variant) normally climbing.
In the uk enroute environment there are currently no procedures to provide wake separation, just 5nm/1000ft or 2000ft where applicable due to non-RVSM airspace. Standard separation is doubled if one aircraft is supersonic, but not due to wake turbulence.