First, don't have your film scanned until you have seen it, unless you enjoy potentially throwing a lot of money down the toilet.
Ektachrome is nowhere near as good at maintaining reciprocity during long exposures as is Fujichrome.
Of course the shots are underexposed. That is what reciprocity failure does, so you would expect that, not overexposure. You did not adjust enough. You need longer exposures.....and/or Fujichrome. No film is designed to be optimized at the effective f stops and exposure times used with pinholes. It is especially hard to get it to work in night shots, as film will not be exposed at all below a certain amount of light, no matter how long the exposure is. You simply need to experiment more. Make sure your effective f stop is properly calculated, first of all.