I think you are adressing one of the real challenges in the field of exosome research - exosome quantitation. As far as I know there is no real consensus regarding which method to use. I know a lot of people measuring protein concentration. In house we have done this as well without lysis of the exosomes. But we have used the Qubit System for protein measurments. However, this might not be the best method due to the fact that also other protein or vesicular structures might have an impact on the protein measurment. Furthermore, many researchers (including our colleagues from Austin Texas) use Nanosight LM10 to measure number of vesicles and size distribution. I do not think this instrument was originally developed for such an application and a lot of optimization is required to get this application up and running, It will also not give you information about any contaminating vesicles in the same size range. On way of checking the presence of contaminating vesicles will be to run WB and e.g. label for gp96, an ER related protein. In terms of sensistivity the ELISA approach sounds like good alternative as well.
It is very challenging and I wish I had a clear answer and advice for you. At the moment I do not think that there are any yet.