Change VertexSize in a big graph

The following work in version 9:

RandomGraph[{1000, 2000}, 
 VertexSize -> Join[{_ -> Scaled[.01]}, Thread[Range[10] -> Scaled[.04]]]]

RandomGraph[{1000, 2000}, 
 VertexSize -> Join[{_ -> 3}, Thread[Range[10] -> 10]]]

Update: For versions 11+ , as shown in halmir's answer, explicit setting of GraphStyle or VertexShapeFunction options gives the desired result. In particular, using the option GraphStyle with any value, e.g.

GraphStyle -> {}
GraphStyle- > "BasicBlue"
GraphStyle-> blah

with the same VertexSize settings as in the examples above gives

You could specify VertexShapeFunction or set GraphStyle -> "Default"

RandomGraph[{1000, 2000}, VertexSize -> 6, VertexShapeFunction -> "Circle"]

RandomGraph[{1000, 2000}, VertexSize -> 5, GraphStyle -> "Default" ]